Cut and Paste can cause References to Disappear
I have a Stack of pages and to the left I have a StackSidebar. The StackSidebar references the stack through its ID which is Pages.
If I cut and paste objects, say onto one of the StackPages, the reference I had in the StackSidebar to the Stack gets removed.
When I had a menu I noticed similar type things with cut in paste but instead of a reference disappearing it would just change to some number that didn't exist. I wasn't using the menu so I just deleted it rather than always deal with it.