diff --git a/bseq/__init__.py b/bseq/__init__.py
index 864fe88..114296c 100644
--- a/bseq/__init__.py
+++ b/bseq/__init__.py
@@ -12,9 +12,13 @@
 @persistent
 def BSEQ_initialize(scene):
     if update_obj not in bpy.app.handlers.frame_change_post:
+        bpy.app.handlers.frame_change_post.append(update_obj)
+    if auto_refresh_active not in bpy.app.handlers.frame_change_post:
         bpy.app.handlers.frame_change_post.append(auto_refresh_active)
+    if auto_refresh_all not in bpy.app.handlers.frame_change_post:
         bpy.app.handlers.frame_change_post.append(auto_refresh_all)
-        bpy.app.handlers.frame_change_post.append(update_obj)
+    if clean_unused_bseq_data not in bpy.app.handlers.save_pre:
+        bpy.app.handlers.save_pre.append(clean_unused_bseq_data)
     subscribe_to_selected()
     if print_information not in bpy.app.handlers.render_init:
         bpy.app.handlers.render_init.append(print_information)
diff --git a/bseq/globals.py b/bseq/globals.py
index 5536bfe..3a7ef10 100644
--- a/bseq/globals.py
+++ b/bseq/globals.py
@@ -51,4 +51,14 @@ def auto_refresh_active(scene, depsgraph=None):
             continue
         if obj.mode != "OBJECT":
             continue
-        refresh_obj(obj, scene)
\ No newline at end of file
+        refresh_obj(obj, scene)
+
+# This becomes necessary, because when deleting objects from the viewport, they dont actually get removed from the
+# sequences list, because this is not a global delete. This handler only removes sequences that are not referenced
+# in any scene or collection. This handler is added to save_pre, so that unused data blocks dont get saved
+def clean_unused_bseq_data(savefile):
+    for obj in bpy.data.objects:
+        if obj.BSEQ.init and len(obj.users_collection)==0 and len(obj.users_scene)==0:
+
+            # This will throw an error if it is actually still used somewhere
+            bpy.data.objects.remove(obj)
\ No newline at end of file
diff --git a/bseq/panels.py b/bseq/panels.py
index d7fc270..6fdd6b1 100644
--- a/bseq/panels.py
+++ b/bseq/panels.py
@@ -13,7 +13,7 @@ def filter_items(self, context, data, property):
         #  not sure if I understand correctly about this
         #  see reference from https://docs.blender.org/api/current/bpy.types.UIList.html#advanced-uilist-example-filtering-and-reordering
         for o in objs:
-            if o.BSEQ.init:
+            if o.BSEQ.init and len(o.users_collection)>0 and len(o.users_scene)>0:
                 flt_flags.append(self.bitflag_filter_item)
             else:
                 flt_flags.append(0)