diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql
new file mode 100644
index 000000000..2238063f4
--- /dev/null
+++ b/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql
@@ -0,0 +1,15 @@
+SELECT core.executeJavaUpgradeCode('reparentOrphanedTargetedMSData');
+
+-- Adding missing foreign keys to core.Containers(EntityId)
+ALTER TABLE targetedms.Runs ADD CONSTRAINT FK_Runs_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.QCAnnotation ADD CONSTRAINT FK_QCAnnotation_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.GuideSet ADD CONSTRAINT FK_GuideSet_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.AutoQCPing ADD CONSTRAINT FK_AutoQCPing_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.PrecursorChromInfo ADD CONSTRAINT FK_PrecursorChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.SampleFileChromInfo ADD CONSTRAINT FK_SampleFileChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+
+-- Adding missing indices on Container
+CREATE INDEX IX_QCAnnotationType_Container ON targetedms.QCAnnotationType(Container);
+CREATE INDEX IX_QCAnnotation_Container ON targetedms.QCAnnotation(Container);
+CREATE INDEX IX_GuideSet_Container ON targetedms.GuideSet(Container);
+CREATE INDEX IX_QCMetricConfiguration_Container ON targetedms.QCMetricConfiguration(Container);
diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java
index 73b423668..ffc7ed5f7 100644
--- a/src/org/labkey/targetedms/TargetedMSManager.java
+++ b/src/org/labkey/targetedms/TargetedMSManager.java
@@ -2524,6 +2524,17 @@ public void moveRun(TargetedMSRun run, Container newContainer, String newRunLSID
 
         new SqlExecutor(getSchema()).execute(updatePrecChromInfoSql);
 
+        SQLFragment updateSampleFileChromInfoSql = new SQLFragment("UPDATE ");
+        updateSampleFileChromInfoSql.append(getTableInfoSampleFileChromInfo(), "");
+        updateSampleFileChromInfoSql.append(" SET container = ?").add(newContainer);
+        updateSampleFileChromInfoSql.append(" WHERE sampleFileId IN (");
+        updateSampleFileChromInfoSql.append(" SELECT sf.Id FROM ").append(getTableInfoSampleFile(), "sf");
+        updateSampleFileChromInfoSql.append(" INNER JOIN ").append(getTableInfoReplicate(), "rep").append(" ON rep.Id = sf.ReplicateId");
+        updateSampleFileChromInfoSql.append(" WHERE rep.runId = ?").add(run.getId());
+        updateSampleFileChromInfoSql.append(" )");
+
+        new SqlExecutor(getSchema()).execute(updateSampleFileChromInfoSql);
+
         run.setExperimentRunLSID(newRunLSID);
         run.setDataId(newDataRowId);
         run.setContainer(newContainer);
diff --git a/src/org/labkey/targetedms/TargetedMSModule.java b/src/org/labkey/targetedms/TargetedMSModule.java
index 921e46202..df82dd64e 100644
--- a/src/org/labkey/targetedms/TargetedMSModule.java
+++ b/src/org/labkey/targetedms/TargetedMSModule.java
@@ -231,7 +231,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.003;
+        return 26.004;
     }
 
     @Override
diff --git a/src/org/labkey/targetedms/TargetedMSUpgradeCode.java b/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
index 3035b5fec..3c95c2dbe 100644
--- a/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
+++ b/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
@@ -108,4 +108,42 @@ public void populatePTMPercentsGroupedPrepivotCache(final ModuleContext moduleCo
 
         LOG.info("Finished populating PTMPercentsGroupedPrepivotCache for existing ExperimentMAM folders");
     }
+
+    @SuppressWarnings("UnusedDeclaration")
+    public void reparentOrphanedTargetedMSData(final ModuleContext moduleContext)
+    {
+        if (moduleContext.isNewInstall())
+        {
+            return;
+        }
+
+        Container sharedContainer = ContainerManager.getSharedContainer();
+
+        SqlExecutor executor = new SqlExecutor(TargetedMSManager.getSchema());
+
+        String[] tablesToDeleteOrphans = {"QCAnnotation", "GuideSet", "AutoQCPing"};
+        for (String tableName : tablesToDeleteOrphans)
+        {
+            SQLFragment deleteSql = new SQLFragment("DELETE FROM targetedms.").append(tableName)
+                    .append(" WHERE Container NOT IN (SELECT EntityId FROM core.Containers)");
+            int deletedCount = executor.execute(deleteSql);
+            if (deletedCount > 0)
+            {
+                LOG.info("Deleted " + deletedCount + " orphaned rows from targetedms." + tableName);
+            }
+        }
+
+        String[] tablesToReparentOrphans = {"Runs", "PrecursorChromInfo", "SampleFileChromInfo"};
+        for (String tableName : tablesToReparentOrphans)
+        {
+            SQLFragment updateSql = new SQLFragment("UPDATE targetedms.").append(tableName)
+                    .append(" SET Container = ? WHERE Container NOT IN (SELECT EntityId FROM core.Containers)")
+                    .add(sharedContainer.getEntityId());
+            int updatedCount = executor.execute(updateSql);
+            if (updatedCount > 0)
+            {
+                LOG.info("Reparented " + updatedCount + " orphaned rows from targetedms." + tableName + " to /Shared");
+            }
+        }
+    }
 }