Sonarr deleting files

I’m using Sonarr Ver. 2.0.0.5054 and it is deleting files during mass renames, as well as incorrectly naming files. I just had it do the entire series of The Middle only to find Episode 1 and 2 of Season 1 not renamed, but there are now fully renames Episodes 1 & 2 but they are not the right ones. Also, in season 3, Episode 1 & 2 are a 2 part but after the mass rename, Episode 1 is gone. I have gone through every setting and cannot find anything that says it should delete any files at any time. On top of all that, it’s moving episodes from one folder to anohter. It moved Season 3 Episode 1 to Season 1 folder and renamed it to S01E01 - Pilot. Any thoughts?

Sounds like the files weren’t linked to the correct files, though that should have been visible when previewing the renames, but it’s impossible to say for certain if that was the case without knowing what Sonarr saw before the rename and what the rename process did ( ((debug logs)) would be the best source for that).

How were the files named before the rename?

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