In case anyone else runs into this problem.
The best solution I’ve found that seems to be working (I’ll update later on if not) is to right click the problem files, and change them to ‘read only’ status. Something is attempting to alter the files.
I have no idea what is causing this to happen - whether it’s an emulator related problem, malware, AV software, or perhaps something windows based that runs on a scheduled task. It did seem like time was a factor more so than number of opens/closes.