Use a separate flag for references deleted by a content file (Fixes #2018)

The flag must be separate so as to not contaminate the user's savegame.

Fixes the following use cases that were broken before:

 - Content file edits a reference that was already deleted by a previously loaded content file -> reference must stay deleted
 - Changed or new content file deletes a reference that is already present in the user's savegame -> reference must be deleted
 - Said content file is disabled again - reference must be undeleted