Renamed TV episode files to add "-01" and "-02" on the end - they disappeared from Plex

Did the Plex dance and it’s working fine - everything is there now.

I doubt it. It would be a matter of deleting files in that directory (or on the library), which is is pretty easy, but then if the rescan were interrupted for some reason, you’d lose data.

There would be an issue with keeping track of what was and wasn’t watched, but I can think of at least 2 ways to do that without even putting thought into it.

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