TV Episodes are being added all over the place, in wrong series... or not added at all

You will need to rescan and you may need to “Plex Dance” the whole series and that usually resets the watched status.

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When you change anything to fix a match it is a good idea to “Plex Dance” the files involved:

1 - Move the media to where Plex cannot see it
2 - Refresh the library
3 - Empty Trash
4 - Clean bundles
5 - Move the series back
6 - Refresh the library

Perform all steps in order and allow each one to finish before starting the next.
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