diff --git a/include/MReadOutAssembly.h b/include/MReadOutAssembly.h
index 1a8b0aa..cc2d210 100644
--- a/include/MReadOutAssembly.h
+++ b/include/MReadOutAssembly.h
@@ -269,10 +269,15 @@ class MReadOutAssembly : public MReadOutSequence
   bool IsStripHitBelowThreshold() const { return m_StripHitBelowThreshold; }
   
 
- //! Set the strip-pairing-incomplete flag
+  //! Set the strip-pairing-incomplete flag
   void SetStripPairingIncomplete(bool Flag = true, MString Text = "") { m_StripPairingIncomplete = Flag;  m_StripPairingIncompleteString = Text; }
   //! Get the strip-pairing-incomplete flag
   bool IsStripPairingIncomplete() const { return m_StripPairingIncomplete; }
+    
+  //! Set the strip-pairing-incomplete flag
+  void SetStripPairingQualityFlag(bool Flag = true, MString Text = "") { m_StripPairingQualityFlag = Flag;  m_StripPairingQualityFlagString = Text; }
+  //! Get the strip-pairing-incomplete flag
+  bool GetStripPairingQualityFlag() const { return m_StripPairingQualityFlag; }
 
   //! Set the LLD Event flag
   void SetLLDEvent(bool Flag = true, MString Text = "") { m_LLDEvent = Flag; m_LLDEventString = Text; }
@@ -453,6 +458,11 @@ class MReadOutAssembly : public MReadOutSequence
   MString m_DepthCalibration_OutofRangeString;
   bool m_StripHitBelowThreshold;
   MString m_StripHitBelowThresholdString;
+    
+  // Flags indicating the quality of the event: quality warning, but not to be filtered out
+  bool m_StripPairingQualityFlag;
+  MString m_StripPairingQualityFlagString;
+
 
 
 
diff --git a/src/MModuleStripPairingMultiRoundChiSquare.cxx b/src/MModuleStripPairingMultiRoundChiSquare.cxx
index a3e42f1..7a75fe1 100644
--- a/src/MModuleStripPairingMultiRoundChiSquare.cxx
+++ b/src/MModuleStripPairingMultiRoundChiSquare.cxx
@@ -272,9 +272,7 @@ bool MModuleStripPairingMultiRoundChiSquare::EventSelection(MReadOutAssembly* Ev
   for (unsigned int d = 0; d < StripHits.size(); ++d) { // Detector loop
     for (unsigned int side = 0; side <= 1; ++side) { // Side loop
       if (StripHits[d][side].size() > MaxStripHits) {
-        Event->SetStripPairingIncomplete(true, "More than 6 hit strips on one side");
-        Event->SetAnalysisProgress(MAssembly::c_StripPairing);
-        return false;
+        Event->SetStripPairingQualityFlag(true, "More than 6 hit strips on one side"); //Only set a quality flag, but don't filter out event
       }
 
       // Check if one side of the detector has no strip hits
@@ -359,11 +357,6 @@ tuple<vector<vector<unsigned int>>, vector<vector<unsigned int>>, double> MModul
 
       unsigned int MinSize = min(Combinations[d][0][lv].size(), Combinations[d][1][hv].size());
 
-      // Skip pairing if either side has more than 5 sets of strips
-      if (max(Combinations[d][0][lv].size(), Combinations[d][1][hv].size()) > MaxCombinations) {
-        continue;
-      }
-
       bool MorePermutations = true;
       while (MorePermutations == true) {
 
@@ -660,9 +653,7 @@ bool MModuleStripPairingMultiRoundChiSquare::CreateHits(unsigned int d, MReadOut
 
   // One last quality selection based on total event energies
   if ((EnergyTotal > max(LVEnergyTotal, HVEnergyTotal) + 2.5 * max(LVEnergyResTotal, HVEnergyResTotal) || EnergyTotal < min(LVEnergyTotal, HVEnergyTotal) - 2.5 * max(LVEnergyResTotal, HVEnergyResTotal))) {
-    Event->SetStripPairingIncomplete(true, "Strips not pairable wihin 2.5 sigma of measured energy");
-    Event->SetAnalysisProgress(MAssembly::c_StripPairing);
-    return false;
+    Event->SetStripPairingQualityFlag(true, "Strips not pairable wihin 2.5 sigma of measured energy"); // Set quality flag, but don't filter out event
   }
   // Plot the good events
   else if ((HasExpos() == true) and Event->IsGood() == true) {
@@ -765,9 +756,12 @@ bool MModuleStripPairingMultiRoundChiSquare::AnalyzeEvent(MReadOutAssembly* Even
     }
     // Flag events with a reduced chi square > 25
     else if (BestChiSquare > 25) {
-      Event->SetStripPairingIncomplete(true, "Best reduced chi square is not below 25");
-      Event->SetAnalysisProgress(MAssembly::c_StripPairing);
-      return false;
+      Event->SetStripPairingQualityFlag(true, "Best reduced chi square is not below 25"); // Set quality flag but don't filter out event
+    }
+      
+    if (max(BestLVSideCombo.size(), BestHVSideCombo.size()) > MaxCombinations) {
+      Event->SetStripPairingQualityFlag(true, "Best LV or HV combination has more than 5 strip groupings");
+      // Set quality flag, but don't filter out event
     }
 
     // Assign the best reduced chi square to the event
diff --git a/src/MReadOutAssembly.cxx b/src/MReadOutAssembly.cxx
index 0c6a9fa..e02848b 100644
--- a/src/MReadOutAssembly.cxx
+++ b/src/MReadOutAssembly.cxx
@@ -184,6 +184,8 @@ void MReadOutAssembly::Clear()
   m_EnergyResolutionCalibrationIncompleteString = "";
   m_StripPairingIncomplete = false;
   m_StripPairingIncompleteString = "";
+  m_StripPairingQualityFlag = false;
+  m_StripPairingQualityFlagString = "";
   m_LLDEvent = false;
   m_LLDEventString = "";
   m_DepthCalibrationIncomplete = false;
@@ -590,6 +592,11 @@ bool MReadOutAssembly::StreamDat(ostream& S, int Version)
     if (m_StripPairingIncompleteString != "") S<<" ("<<m_StripPairingIncompleteString<<")";
     S<<endl;
   }
+  if (m_StripPairingQualityFlag == true) {
+    S<<"QA StripPairingQualityFlag";
+    if (m_StripPairingQualityFlagString != "") S<<" ("<<m_StripPairingQualityFlagString<<")";
+    S<<endl;
+    }
   if (m_LLDEvent == true) {
     S<<"BD LLDEvent";
     if (m_LLDEventString != "") S<<" ("<<m_LLDEventString<<")";
@@ -614,13 +621,13 @@ bool MReadOutAssembly::StreamDat(ostream& S, int Version)
   }
   for (auto H : m_Hits) {
     if (H->GetStripHitMultipleTimesX()) {
-      S<<"BD Multiple Hits on LV Strip"<<endl;
+      S<<"QA Multiple Hits on LV Strip"<<endl;
       break;
     }
   }
   for (auto H : m_Hits) {
     if (H->GetStripHitMultipleTimesY()) {
-      S<<"BD Multiple Hits on HV Strip"<<endl;
+      S<<"QA Multiple Hits on HV Strip"<<endl;
       break;
     }
   }
@@ -690,6 +697,11 @@ void MReadOutAssembly::StreamEvta(ostream& S)
     if (m_StripPairingIncompleteString != "") S<<" ("<<m_StripPairingIncompleteString<<")";
     S<<endl;
   }
+  if (m_StripPairingQualityFlag == true) {
+    S<<"QA StripPairingQualityFlag";
+    if (m_StripPairingQualityFlagString != "") S<<" ("<<m_StripPairingQualityFlagString<<")";
+    S<<endl;
+    }
   if (m_LLDEvent == true) {
     S<<"BD LLDEvent";
     if (m_LLDEventString != "") S<<" ("<<m_LLDEventString<<")";
@@ -714,13 +726,13 @@ void MReadOutAssembly::StreamEvta(ostream& S)
   }
   for (auto H : m_Hits) {
     if (H->GetStripHitMultipleTimesX()) {
-      S<<"BD Multiple Hits on LV Strip"<<endl;
+      S<<"QA Multiple Hits on LV Strip"<<endl;
       break;
     }
   }
   for (auto H : m_Hits) {
     if (H->GetStripHitMultipleTimesY()) {
-      S<<"BD Multiple Hits on HV Strip"<<endl;
+      S<<"QA Multiple Hits on HV Strip"<<endl;
       break;
     }
   }