diff --git a/src/Jobs/Handler/Files.hs b/src/Jobs/Handler/Files.hs
index 6c44b230d..0427b001d 100644
--- a/src/Jobs/Handler/Files.hs
+++ b/src/Jobs/Handler/Files.hs
@@ -47,6 +47,8 @@ import Control.Concurrent.STM.TVar (stateTVar)
 
 import qualified Data.Foldable as F
 
+import qualified Control.Monad.State.Class as State
+
 
 dispatchJobPruneSessionFiles :: JobHandler UniWorX
 dispatchJobPruneSessionFiles = JobHandlerAtomicWithFinalizer act fin
@@ -76,10 +78,11 @@ fileReferences (E.just -> fHash)
              E.&&. chunkLock E.^. FileChunkLockHash E.==. E.subSelectForeign fileContentEntry FileContentEntryChunkHash (E.^. FileContentChunkHash)
     ]
 
-workflowFileReferences :: MonadResource m => ConduitT () FileContentReference (SqlPersistT m) ()
-workflowFileReferences = mconcat [ E.selectSource (E.from $ pure . (E.^. SharedWorkflowGraphGraph)) .| awaitForever (mapMOf_ (typesCustom @WorkflowChildren . _fileReferenceContent . _Just) yield . E.unValue)
-                                 , E.selectSource (E.from $ pure . (E.^. WorkflowWorkflowState  )) .| awaitForever (mapMOf_ (typesCustom @WorkflowChildren . _fileReferenceContent . _Just) yield . E.unValue)
-                                 ]
+workflowFileReferences :: MonadResource m => Map Text (ConduitT () FileContentReference (SqlPersistT m) ())
+workflowFileReferences = Map.fromList $ over (traverse . _1) nameToPathPiece
+  [ (''SharedWorkflowGraph, E.selectSource (E.from $ pure . (E.^. SharedWorkflowGraphGraph)) .| awaitForever (mapMOf_ (typesCustom @WorkflowChildren . _fileReferenceContent . _Just) yield . E.unValue))
+  , (''WorkflowWorkflow,    E.selectSource (E.from $ pure . (E.^. WorkflowWorkflowState  )) .| awaitForever (mapMOf_ (typesCustom @WorkflowChildren . _fileReferenceContent . _Just) yield . E.unValue))
+  ]
 
 
 dispatchJobDetectMissingFiles :: JobHandler UniWorX
@@ -89,15 +92,20 @@ dispatchJobDetectMissingFiles = JobHandlerAtomicWithFinalizer act fin
     act = hoist lift $ do
       uploadBucket <- getsYesod $ view _appUploadCacheBucket
 
-      missingDb <- execWriterT $ do
-        tellM . forM trackedReferences $ \refQuery ->
-          fmap (Set.fromList . mapMaybe E.unValue) . E.select $ do
-            ref <- refQuery
-            E.where_ . E.not_ $ E.isNothing ref
-            E.where_ . E.not_ . E.exists . E.from $ \fileContentEntry ->
-              E.where_ $ E.just (fileContentEntry E.^. FileContentEntryHash) E.==. ref
-            E.distinctOnOrderBy [E.asc ref] $ return ref
-        tellM . fmap (Map.singleton "workflows") . runConduit $ workflowFileReferences .| C.foldMap Set.singleton
+      missingDb <- runConduit . execStateC Map.empty $ do
+        let insertRef refKind ref = State.modify' $ Map.alter (Just . Set.insert ref . fromMaybe Set.empty) refKind
+        
+        iforM_ trackedReferences $ \refKind refQuery -> do
+          let fileReferencesQuery = do
+                ref <- refQuery
+                E.where_ . E.not_ $ E.isNothing ref
+                E.where_ . E.not_ . E.exists . E.from $ \fileContentEntry ->
+                  E.where_ $ E.just (fileContentEntry E.^. FileContentEntryHash) E.==. ref
+                E.distinctOnOrderBy [E.asc ref] $ return ref
+          transPipe lift (E.selectSource fileReferencesQuery) .| C.mapMaybe E.unValue .| C.mapM_ (insertRef refKind)
+
+        iforM_ workflowFileReferences $ \refKind refSource ->
+          transPipe lift (refSource .| C.filterM (\ref -> not <$> exists [FileContentEntryHash ==. ref])) .| C.mapM_ (insertRef refKind)
 
       let allMissingDb :: Set Minio.Object
           allMissingDb = setOf (folded . folded . re minioFileReference) missingDb
@@ -123,12 +131,13 @@ dispatchJobDetectMissingFiles = JobHandlerAtomicWithFinalizer act fin
 
     fin :: Map Text (NonNull (Set FileContentReference)) -> Handler ()
     fin missingCounts = do
-      forM_ (Map.keysSet trackedReferences) $ \refIdent ->
-        observeMissingFiles refIdent . maybe 0 olength $ missingCounts Map.!? refIdent
+      imapM_ observeMissingFiles $ olength <$> missingCounts
 
       iforM_ missingCounts $ \refIdent missingFiles
-        -> let missingRefs = unlines . map tshow . Set.toList $ toNullable missingFiles
-            in $logErrorS "MissingFiles" [st|#{refIdent}: #{olength missingFiles}\n#{missingRefs}|]
+        -> let missingRefs = unlines . map (views _Wrapped tshow) . Set.toList $ toNullable missingFiles
+               newl :: Text
+               newl = "\n"
+            in $logErrorS "MissingFiles" [st|#{refIdent}: #{olength missingFiles}#{newl}#{missingRefs}|]
 
       when (Map.null missingCounts) $
         $logInfoS "MissingFiles" [st|No missing files|]
@@ -201,7 +210,7 @@ dispatchJobPruneUnreferencedFiles numIterations epoch iteration = JobHandlerAtom
               return $ fileContentEntry E.^. FileContentEntryHash `E.in_` E.valList fRefs 
             E.where_ . chunkIdFilter $ E.subSelectForeign fileContentChunkUnreferenced FileContentChunkUnreferencedHash (E.^. FileContentChunkHash)
           chunkSize = 100
-       in runConduit $ workflowFileReferences .| C.map Seq.singleton .| C.chunksOfE chunkSize .| C.mapM_ unmarkWorkflowFiles
+       in runConduit $ sequence_ workflowFileReferences .| C.map Seq.singleton .| C.chunksOfE chunkSize .| C.mapM_ unmarkWorkflowFiles
   
       let
         getEntryCandidates = E.selectSource . E.from $ \fileContentEntry -> do