diff --git a/SleepLib/calcs.cpp b/SleepLib/calcs.cpp
index e5849c2a..4cb1986b 100644
--- a/SleepLib/calcs.cpp
+++ b/SleepLib/calcs.cpp
@@ -213,7 +213,6 @@ void FlowParser::calcPeaks(EventDataType * input, int samples)
 
     EventDataType zeroline=0;
 
-    // For each sample in flow waveform
     double rate=m_flow->rate();
 
     double flowstart=m_flow->first();
@@ -240,17 +239,13 @@ void FlowParser::calcPeaks(EventDataType * input, int samples)
 
 
     int sps=1000/m_rate;
-    // For each samples, find the peak upper and lower breath components
-    //bool dirty=false;
     int len=0, lastk=0; //lastlen=0
 
-    //EventList *uf2=m_session->AddEventList(CPAP_UserFlag2,EVL_Event);
-
     qint64 sttime=time;//, ettime=time;
 
+    // For each samples, find the peak upper and lower breath components
     for (int k=0; k < samples; k++) {
         c=input[k];
-      //  dirty=false;
 
         if (c >= zeroline) {
 
@@ -262,14 +257,7 @@ void FlowParser::calcPeaks(EventDataType * input, int samples)
 
                     // peak detection may not be needed..
                     breaths.push_back(BreathPeak(min, max, start, middle, k)); //, peakmin, peakmax));
-                    //EventDataType g0=(0-lastc) / (c-lastc);
-                    //double d=(m_rate*g0);
-                    //double d1=flowstart+ (start*rate);
-                    //double d2=peakmax;
 
-                    //uf1->AddEvent(d1,0);
-                    //uf2->AddEvent(d2,0);
-                    //lastlen=k-start;
                     // Set max for start of the upper breath cycle
                     max=c;
                     peakmax=time;
@@ -278,11 +266,7 @@ void FlowParser::calcPeaks(EventDataType * input, int samples)
                     // Starting point of next breath cycle
                     start=k;
                     sttime=time;
-                }/* else {
-                    if ((max <=3) || ((max-min) <= 8)) {
-                        start=k;
-                    }
-                }*/
+                }
             } else if (c > max) {
                 // Update upper breath peak
                 max=c;
@@ -308,7 +292,6 @@ void FlowParser::calcPeaks(EventDataType * input, int samples)
         }
         lasttime=time;
         time+=rate;
-        //if (!dirty)
         lastc=c;
         lastk=k;
     }
diff --git a/SleepLib/profiles.h b/SleepLib/profiles.h
index 1ce50018..d293a8aa 100644
--- a/SleepLib/profiles.h
+++ b/SleepLib/profiles.h
@@ -370,7 +370,7 @@ public:
         if (!m_profile->contains(STR_CS_UntreatedAHI)) (*m_profile)[STR_CS_UntreatedAHI]=0.0;
         if (!m_profile->contains(STR_CS_Notes)) (*m_profile)[STR_CS_Notes]=QString();
         if (!m_profile->contains(STR_CS_DateDiagnosed)) (*m_profile)[STR_CS_DateDiagnosed]=QDate();
-        if (!m_profile->contains(STR_CS_UserFlowRestriction)) (*m_profile)[STR_CS_UserFlowRestriction]=10.0;
+        if (!m_profile->contains(STR_CS_UserFlowRestriction)) (*m_profile)[STR_CS_UserFlowRestriction]=20.0;
         if (!m_profile->contains(STR_CS_UserEventDuration)) (*m_profile)[STR_CS_UserEventDuration]=10.0;
         if (!m_profile->contains(STR_CS_UserEventFlagging)) (*m_profile)[STR_CS_UserEventFlagging]=false;
         if (!m_profile->contains(STR_CS_AHIWindow)) (*m_profile)[STR_CS_AHIWindow]=60.0;
diff --git a/SleepLib/session.cpp b/SleepLib/session.cpp
index b5505724..dce31455 100644
--- a/SleepLib/session.cpp
+++ b/SleepLib/session.cpp
@@ -644,6 +644,31 @@ bool Session::LoadEvents(QString filename)
     return true;
 }
 
+void Session::destroyEvent(ChannelID code)
+{
+    QHash<ChannelID,QVector<EventList *> >::iterator it=eventlist.find(code);
+    if (it!=eventlist.end()) {
+        for (int i=0;i<it.value().size();i++) {
+            delete it.value()[i];
+        }
+        eventlist.erase(it);
+    }
+    m_gain.erase(m_gain.find(code));
+    m_firstchan.erase(m_firstchan.find(code));
+    m_lastchan.erase(m_lastchan.find(code));
+    m_sph.erase(m_sph.find(code));
+    m_cph.erase(m_cph.find(code));
+    m_min.erase(m_min.find(code));
+    m_max.erase(m_max.find(code));
+    m_avg.erase(m_avg.find(code));
+    m_wavg.erase(m_wavg.find(code));
+    m_sum.erase(m_sum.find(code));
+    m_cnt.erase(m_cnt.find(code));
+    m_valuesummary.erase(m_valuesummary.find(code));
+    m_timesummary.erase(m_timesummary.find(code));
+    // does not trash settings..
+}
+
 void Session::updateCountSummary(ChannelID code)
 {
     QHash<ChannelID,QVector<EventList *> >::iterator ev=eventlist.find(code);
@@ -918,6 +943,18 @@ qint64 Session::last(ChannelID id)
     m_lastchan[id]=max;
     return max;
 }
+bool Session::channelDataExists(ChannelID id)
+{
+    if (s_events_loaded) {
+        QHash<ChannelID,QVector<EventList *> >::iterator j=eventlist.find(id);
+        if (j==eventlist.end())  // eventlist not loaded.
+            return false;
+        return true;
+    } else {
+        qDebug() << "Calling channelDataExists without open eventdata!";
+    }
+    return false;
+}
 bool Session::channelExists(ChannelID id)
 {
     if (!enabled()) return false;
diff --git a/SleepLib/session.h b/SleepLib/session.h
index 29ada22c..431498a5 100644
--- a/SleepLib/session.h
+++ b/SleepLib/session.h
@@ -154,8 +154,12 @@ public:
     QHash<ChannelID,QHash<EventStoreType, quint32> > m_timesummary;
     QHash<ChannelID,EventDataType> m_gain;
 
+    //! \brief Generates sum and time data for each distinct value in 'code' events..
     void updateCountSummary(ChannelID code);
 
+    //! \brief Destroy any trace of event 'code', freeing any memory if loaded.
+    void destroyEvent(ChannelID code);
+
     // UpdateSummaries may recalculate all these, but it may be faster setting upfront
     void setCount(ChannelID id,int val) { m_cnt[id]=val; }
     void setSum(ChannelID id,EventDataType val) { m_sum[id]=val; }
@@ -222,6 +226,9 @@ public:
     //! \brief Returns true if the channel has events loaded, or a record of a count for when they are not
     bool channelExists(ChannelID name);
 
+    //! \brief Returns true if the channel has event data available (must be loaded first)
+    bool channelDataExists(ChannelID id);
+
     bool IsLoneSession() { return s_lonesession; }
     void SetLoneSession(bool b) { s_lonesession=b; }
 
diff --git a/mainwindow.cpp b/mainwindow.cpp
index 0ed52669..e5e440ef 100644
--- a/mainwindow.cpp
+++ b/mainwindow.cpp
@@ -33,8 +33,10 @@
 #include "SleepLib/schema.h"
 #include "Graphs/glcommon.h"
 #include "UpdaterWindow.h"
+#include "SleepLib/calcs.h"
 #include "version.h"
 
+
 QProgressBar *qprogress;
 QLabel *qstatus;
 QLabel *qstatus2;
@@ -89,6 +91,8 @@ MainWindow::MainWindow(QWidget *parent) :
     oximetry=NULL;
     prefdialog=NULL;
 
+    m_inRecalculation=false;
+    m_restartRequired=false;
     // Initialize Status Bar objects
     qstatusbar=ui->statusbar;
     qprogress=new QProgressBar(this);
@@ -153,6 +157,10 @@ MainWindow::MainWindow(QWidget *parent) :
     ui->toolBox->setCurrentIndex(0);
     daily->graphView()->redraw();
 
+    if (PROFILE.cpap->AHIWindow() < 30.0) {
+        PROFILE.cpap->setAHIWindow(60.0);
+    }
+
     ui->recordsBox->page()->setLinkDelegationPolicy(QWebPage::DelegateAllLinks);
     ui->summaryView->page()->setLinkDelegationPolicy(QWebPage::DelegateAllLinks);
     ui->webView->page()->setLinkDelegationPolicy(QWebPage::DelegateExternalLinks);
@@ -1423,11 +1431,15 @@ void MainWindow::on_action_Reset_Graph_Layout_triggered()
 
 void MainWindow::on_action_Preferences_triggered()
 {
+    if (m_inRecalculation) {
+        mainwin->Notify("Access to Preferences has been blocked until recalculation completes.");
+        return;
+    }
     PreferencesDialog pd(this,p_profile);
     prefdialog=&pd;
     if (pd.exec()==PreferencesDialog::Accepted) {
         qDebug() << "Preferences Accepted";
-        pd.Save();
+        //pd.Save();
         if (daily) {
             //daily->ReloadGraphs();
             daily->RedrawGraphs();
@@ -2400,30 +2412,6 @@ void MainWindow::on_webView_linkClicked(const QUrl &url)
     }
 }
 
-//void MainWindow::on_favouritesList_itemSelectionChanged()
-//{
-//    QListWidgetItem *item=ui->favouritesList->currentItem();
-//    if (!item) return;
-//    QDate date=item->data(Qt::UserRole).toDate();
-//    if (date.isValid()) {
-//        daily->LoadDate(date);
-//        ui->tabWidget->setCurrentWidget(daily);
-//    }
-//}
-
-/*void MainWindow::on_favouritesList_itemClicked(QListWidgetItem *item)
-{
-    if (!item) return;
-    QDate date=item->data(Qt::UserRole).toDate();
-    if (date.isValid()) {
-        if (date==daily->getDate()) {
-            ui->tabWidget->setCurrentWidget(daily);
-            daily->graphView()->ResetBounds();
-            daily->graphView()->redraw();
-        }
-    }
-}*/
-
 void MainWindow::on_webView_statusBarMessage(const QString &text)
 {
     ui->statusbar->showMessage(text);
@@ -2479,3 +2467,83 @@ void MainWindow::on_filterBookmarksButton_clicked()
         updateFavourites();
     }
 }
+
+void MainWindow::reprocessEvents(bool restart)
+{
+    m_restartRequired=restart;
+    QTimer::singleShot(0,this,SLOT(doReprocessEvents()));
+}
+
+
+void MainWindow::doReprocessEvents()
+{
+    m_inRecalculation=true;
+    QDate first=PROFILE.FirstDay();
+    QDate date=PROFILE.LastDay();
+    Session *sess;
+    Day *day;
+    //FlowParser flowparser;
+    if (m_restartRequired) {
+        QMessageBox::information(this,"Restart Required",QString("The application will automatically restart after the following reindexing operation"),QMessageBox::Ok);
+    }
+
+    mainwin->Notify("Performance will be degraded during these recalculations.","Recalculating Indicdes");
+
+    bool isopen;
+    // For each day in history
+    int daycount=first.daysTo(date);
+    int idx=0;
+    if (qprogress) {
+        qstatus->setText(tr("Recalculating Summaries"));
+        qprogress->setValue(0);
+        qprogress->setVisible(true);
+    }
+    do {
+        day=PROFILE.GetDay(date,MT_CPAP);
+        if (day) {
+            for (int i=0;i<day->size();i++) {
+                sess=(*day)[i];
+                isopen=sess->eventsLoaded();
+                // Load the events
+                sess->OpenEvents();
+
+                //if (!sess->channelDataExists(CPAP_FlowRate)) continue;
+
+                //QVector<EventList *> & flowlist=sess->eventlist[CPAP_FlowRate];
+
+                // Destroy any current user flags..
+                sess->destroyEvent(CPAP_UserFlag1);
+                sess->destroyEvent(CPAP_UserFlag2);
+                sess->destroyEvent(CPAP_UserFlag3);
+
+                // AHI flags
+                sess->destroyEvent(CPAP_AHI);
+
+//                for (int j=0;j<flowlist.size();j++) {
+//                    flowparser.openFlow(sess,flowlist[j]);
+//                    flowparser.flagEvents();
+//                }
+                sess->UpdateSummaries();
+                sess->SetChanged(true);
+                sess->machine()->SaveSession(sess);
+                if (!isopen) sess->TrashEvents();
+            }
+        }
+        date=date.addDays(-1);
+       // if (qprogress && (++idx % 10) ==0) {
+            qprogress->setValue(0+(float(++idx)/float(daycount)*100.0));
+            QApplication::processEvents();
+       // }
+
+    } while (date>=first);
+    qstatus->setText(tr(""));
+    qprogress->setVisible(false);
+    if (!m_restartRequired) {
+        if (overview) overview->ReloadGraphs();
+        daily->ReloadGraphs();
+    } else {
+        RestartApplication();
+    }
+    m_inRecalculation=false;
+    mainwin->Notify("Recalculations are now complete.","Recalculating Indicdes");
+}
diff --git a/mainwindow.h b/mainwindow.h
index 69d3cf45..8558c60a 100644
--- a/mainwindow.h
+++ b/mainwindow.h
@@ -88,7 +88,6 @@ public:
     //! \brief Refresh the statistics page
     void refreshStatistics() { on_summaryButton_clicked(); }
 
-
     /*! \fn Notify(QString s,int ms=5000, QString title="SleepyHead v"+VersionString());
         \brief Pops up a message box near the system tray
         \param QString string
@@ -138,6 +137,14 @@ public:
     void PrintReport(gGraphView *gv,QString name, QDate date=QDate::currentDate());
 
     void sendStatsUrl(QString msg) { on_recordsBox_linkClicked(QUrl(msg)); }
+
+    //! \brief Sets up recalculation of all event summaries and flags
+    void reprocessEvents(bool restart=false);
+
+public slots:
+    //! \brief Recalculate all event summaries and flags
+    void doReprocessEvents();
+
 protected:
     virtual void keyPressEvent(QKeyEvent * event);
 
@@ -298,6 +305,8 @@ private:
     QMenu *systraymenu;
     gGraphView *SnapshotGraph;
     QString bookmarkFilter;
+    bool m_restartRequired;
+    volatile bool m_inRecalculation;
 };
 
 #endif // MAINWINDOW_H
diff --git a/preferencesdialog.cpp b/preferencesdialog.cpp
index ff13db5c..a37bf555 100644
--- a/preferencesdialog.cpp
+++ b/preferencesdialog.cpp
@@ -10,7 +10,6 @@
 #include "preferencesdialog.h"
 #include "common_gui.h"
 
-
 #include <Graphs/gGraphView.h>
 #include <mainwindow.h>
 #include "ui_preferencesdialog.h"
@@ -43,7 +42,6 @@ PreferencesDialog::PreferencesDialog(QWidget *parent,Profile * _profile) :
     ui->leakProfile->setColumnWidth(0,100);
     ui->maskTypeCombo->clear();
 
-    //ui->ahiGraphGroupbox->setEnabled(false);
     //ui->customEventGroupbox->setEnabled(false);
 
     QString masktype=tr("Nasal Pillows");
@@ -194,6 +192,7 @@ PreferencesDialog::PreferencesDialog(QWidget *parent,Profile * _profile) :
     if (ot<0) ot=0;
     ui->oximetryType->setCurrentIndex(ot);
 
+    ui->ahiGraphWindowSize->setEnabled(false);
     ui->ahiGraphWindowSize->setValue(profile->cpap->AHIWindow());
     ui->ahiGraphZeroReset->setChecked(profile->cpap->AHIReset());
 
@@ -276,15 +275,48 @@ void PreferencesDialog::on_eventTable_doubleClicked(const QModelIndex &index)
     }
 }
 
-void PreferencesDialog::Save()
+bool PreferencesDialog::Save()
 {
+    bool recalc_events=false;
     bool needs_restart=false;
 
-    profile->appearance->setAntiAliasing(ui->useAntiAliasing->isChecked());
+    if (ui->ahiGraphZeroReset->isChecked()!=profile->cpap->AHIReset()) recalc_events=true;
+
     if (ui->useSquareWavePlots->isChecked()!=profile->appearance->squareWavePlots()) {
-        profile->appearance->setSquareWavePlots(ui->useSquareWavePlots->isChecked());
         needs_restart=true;
     }
+    if ((profile->session->daySplitTime()!=ui->timeEdit->time()) ||
+        (profile->session->combineCloseSessions()!=ui->combineSlider->value()) ||
+        (profile->session->ignoreShortSessions()!=ui->IgnoreSlider->value())) {
+        needs_restart=true;
+    }
+    if (profile->general->calculateRDI() != ui->AddRERAtoAHI->isChecked()) {
+        recalc_events=true;
+        needs_restart=true;
+    }
+    if (profile->cpap->userEventFlagging() &&
+       (profile->cpap->userEventDuration()!=ui->apneaDuration->value() ||
+        profile->cpap->userFlowRestriction()!=ui->apneaFlowRestriction->value()))
+        recalc_events=true;
+
+    // Restart if turning user event flagging on/off
+    if (profile->cpap->userEventFlagging()!=ui->customEventGroupbox->isChecked()) {
+        if (!profile->cpap->userEventFlagging()) // Don't bother recalculating, just switch off
+            needs_restart=true;
+        else recalc_events=true;
+    }
+    if (recalc_events) {
+        if (QMessageBox::question(this,tr("Data Reindex Required"),tr("A lengthy data reindexing proceedure is required to apply these changes.\n\nAre you sure you want to make these changes?"),QMessageBox::Yes,QMessageBox::No)==QMessageBox::No) {
+            return false;
+        }
+    } else if (needs_restart) {
+        if (QMessageBox::question(this,tr("Restart Required"),tr("One or more of the changes you have made will require this application to be restarted,\nin order for these changes to come into effect.\n\nWould you like do this now?"),QMessageBox::Yes,QMessageBox::No)==QMessageBox::No) {
+            return false;
+        }
+    }
+
+    profile->appearance->setAntiAliasing(ui->useAntiAliasing->isChecked());
+    profile->appearance->setSquareWavePlots(ui->useSquareWavePlots->isChecked());
     profile->appearance->setGraphSnapshots(ui->enableGraphSnapshots->isChecked());
     profile->general->setSkipEmptyDays(ui->skipEmptyDays->isChecked());
     profile->session->setMultithreading(ui->enableMultithreading->isChecked());
@@ -298,16 +330,8 @@ void PreferencesDialog::Save()
     profile->cpap->setMaskStartDate(ui->startedUsingMask->date());
     profile->appearance->setGraphHeight(ui->graphHeight->value());
 
-    if ((profile->session->daySplitTime()!=ui->timeEdit->time()) ||
-    (profile->session->combineCloseSessions()!=ui->combineSlider->value()) ||
-    (profile->session->ignoreShortSessions()!=ui->IgnoreSlider->value())) {
-        needs_restart=true;
-    }
 
-    if (profile->general->calculateRDI() != ui->AddRERAtoAHI->isChecked()) {
-        profile->general->setCalculateRDI(ui->AddRERAtoAHI->isChecked());
-        needs_restart=true;
-    }
+    profile->general->setCalculateRDI(ui->AddRERAtoAHI->isChecked());
     profile->session->setBackupCardData(ui->createSDBackups->isChecked());
     profile->session->setCompressBackupData(ui->compressSDBackups->isChecked());
     profile->session->setCompressSessionData(ui->compressSessionData->isChecked());
@@ -348,11 +372,9 @@ void PreferencesDialog::Save()
     profile->cpap->setAHIWindow(ui->ahiGraphWindowSize->value());
     profile->cpap->setAHIReset(ui->ahiGraphZeroReset->isChecked());
 
-    // Restart if turning user event flagging on/off
-    if (profile->cpap->userEventFlagging()!=ui->customEventGroupbox->isChecked())
-        needs_restart=true;
 
     profile->cpap->setUserEventFlagging(ui->customEventGroupbox->isChecked());
+
     profile->cpap->setUserEventDuration(ui->apneaDuration->value());
     profile->cpap->setUserFlowRestriction(ui->apneaFlowRestriction->value());
 
@@ -428,11 +450,15 @@ void PreferencesDialog::Save()
     //PROFILE.Save();
     //PREF.Save();
 
-    if (needs_restart) {
-        if (QMessageBox::question(this,tr("Restart Required"),tr("One or more of the changes you have made will require this application to be restarted, in order for these changes to come into effect.\nWould you like do this now?"),QMessageBox::Yes,QMessageBox::No)==QMessageBox::Yes) {
+    if (recalc_events) {
+        // send a signal instead?
+        mainwin->reprocessEvents(needs_restart);
+    } else {
+        if (needs_restart) {
             mainwin->RestartApplication();
         }
     }
+    return true;
 }
 
 void PreferencesDialog::on_combineSlider_valueChanged(int position)
@@ -758,3 +784,9 @@ void PreferencesDialog::on_createSDBackups_toggled(bool checked)
     if (!checked) ui->compressSDBackups->setChecked(false);
     ui->compressSDBackups->setEnabled(checked);
 }
+
+void PreferencesDialog::on_okButton_clicked()
+{
+    if (Save())
+        accept();
+}
diff --git a/preferencesdialog.h b/preferencesdialog.h
index c2cb16da..83be6cfc 100644
--- a/preferencesdialog.h
+++ b/preferencesdialog.h
@@ -57,8 +57,8 @@ public:
     explicit PreferencesDialog(QWidget *parent, Profile * _profile);
     ~PreferencesDialog();
 
-    //! \brief Save the current preferences, called when Ok button is clicked on
-    void Save();
+    //! \brief Save the current preferences, called when Ok button is clicked on.
+    bool Save();
 
     //! \brief Updates the date text of the last time updates where checked
     void RefreshLastChecked();
@@ -89,6 +89,8 @@ private slots:
 
     void on_createSDBackups_toggled(bool checked);
 
+    void on_okButton_clicked();
+
 private:
     //! \brief Populates the Graph Model view with data from the Daily, Overview & Oximetry gGraphView objects
     void resetGraphModel();
diff --git a/preferencesdialog.ui b/preferencesdialog.ui
index 285684da..f61ee443 100644
--- a/preferencesdialog.ui
+++ b/preferencesdialog.ui
@@ -2184,22 +2184,6 @@ It really doesn't use that much resources.. :)</string>
   <include location="Resources.qrc"/>
  </resources>
  <connections>
-  <connection>
-   <sender>okButton</sender>
-   <signal>clicked()</signal>
-   <receiver>PreferencesDialog</receiver>
-   <slot>accept()</slot>
-   <hints>
-    <hint type="sourcelabel">
-     <x>632</x>
-     <y>387</y>
-    </hint>
-    <hint type="destinationlabel">
-     <x>157</x>
-     <y>274</y>
-    </hint>
-   </hints>
-  </connection>
   <connection>
    <sender>cancelButton</sender>
    <signal>clicked()</signal>