One File Per Actor - Can't save deletions in 5.0

Currently working on a project where I can’t delete anything. The project is using One File Per Actor, I have it enabled in the Editor Preferences and in the World Settings. I am also using Source Control. I can add new actors and I can someone reliably move existing actors, but I can’t remove them. If I do and I save, I’ll typically get a dialog window asking me what to save and when I do it pretends to do some clean up of old files.

Has anyone experienced this? Has anyone found a work around? We’re planning to transition to 5.1 in the new year, but thats a long ways a way.