diff --git a/source/blender/blenkernel/intern/collection.c b/source/blender/blenkernel/intern/collection.c
index 5eec788255d..69fd682203f 100644
--- a/source/blender/blenkernel/intern/collection.c
+++ b/source/blender/blenkernel/intern/collection.c
@@ -1773,6 +1773,15 @@ static void layer_collection_flags_store(Main *bmain,
   }
 }
 
+static void layer_collection_flags_free_recursive(LayerCollectionFlag *flag)
+{
+  LISTBASE_FOREACH (LayerCollectionFlag *, child, &flag->children) {
+    layer_collection_flags_free_recursive(child);
+  }
+
+  BLI_freelistN(&flag->children);
+}
+
 static void layer_collection_flags_restore_recursive(LayerCollection *layer_collection,
                                                      LayerCollectionFlag *flag)
 {
@@ -1788,7 +1797,6 @@ static void layer_collection_flags_restore_recursive(LayerCollection *layer_coll
 
     child_flag = child_flag->next;
   }
-  BLI_freelistN(&flag->children);
 
   /* We treat exclude as a special case.
    *
@@ -1814,10 +1822,13 @@ static void layer_collection_flags_restore(ListBase *flags, const Collection *co
 
     LayerCollection *layer_collection = BKE_layer_collection_first_from_scene_collection(
         view_layer, collection);
-    /* The flags should only be added if the collection is in the view layer. */
-    BLI_assert(layer_collection != NULL);
-
-    layer_collection_flags_restore_recursive(layer_collection, flag);
+    /* The flags should only be added if the collection is the scene in the first place, which
+     * means that it should also be in the view layer. However, in "Linked Copy" scenes where the
+     * moved collection is completely removed from the heirarchy. */
+    if (layer_collection != NULL) {
+      layer_collection_flags_restore_recursive(layer_collection, flag);
+    }
+    layer_collection_flags_free_recursive(flag);
   }
 
   BLI_freelistN(flags);