So while waiting on a response (not a complaint of waiting for response, just a statement) I did some more research and noticed that the files in question are ALWAYS photos.
To give some background I’m using calibre so I have folder X with 3 files, one of which is a cover as a .jpg. When I make a change to the author/name in calibre it moves it to a new folder and then deletes the original. The problem is that it’s using hardlinks for the move to help ensure files don’t just vanish during the move (and it’s doing this for ALL the files, not just the problem ones) so suddenly something happens on the EX4 and I can no longer move the file as it’s saying they’re the same file. Both of the other files are being moved in the exact same manner and are having absolutely no issues whatsoever and I was running this method for 2 months now with my EX4 without any issue overall until 1.03.39. I did notice that wdphotodbmerger was running a lot so I’m wondering if that is what is causing the issue as maybe it is trying to scan the “new” image as soon as it shows up.
If this is the case how to I permenantly disable wdphotodbmerger as I don’t want nor need any wd process to do anything to my photos that are on the system.