diff --git a/src/org/labkey/targetedms/TargetedMSDataHandler.java b/src/org/labkey/targetedms/TargetedMSDataHandler.java
index f36b7661e..90501b0ad 100644
--- a/src/org/labkey/targetedms/TargetedMSDataHandler.java
+++ b/src/org/labkey/targetedms/TargetedMSDataHandler.java
@@ -32,6 +32,7 @@
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineService;
+import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.targetedms.RunRepresentativeDataState;
 import org.labkey.api.targetedms.TargetedMSService;
@@ -285,6 +286,26 @@ public void runMoved(ExpData newData, Container container, Container targetConta
             newData.save(user);
         }
 
+        // Fix ExpRun's FilePathRoot if it is still set to the file root of the source folder
+        ExpRun experimentRun = ExperimentService.get().getExpRun(newRunLSID);
+        if (experimentRun == null)
+        {
+            throw new ExperimentException("Unable to find exprun for lsid " + newRunLSID + ". Cannot set the filePathRoot.");
+        }
+        Path newFileRootPath = targetRoot.getRootFileLike().toNioPathForRead();
+        if (!newFileRootPath.equals(experimentRun.getFilePathRootPath()))
+        {
+            experimentRun.setFilePathRootPath(newFileRootPath);
+            try
+            {
+                experimentRun.save(user);
+            }
+            catch (BatchValidationException e)
+            {
+                throw new ExperimentException(e);
+            }
+        }
+
         // Update the run
         TargetedMSManager.moveRun(run, targetContainer, newRunLSID, newData.getRowId(), user);