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Yep TVDB is the answer here. I had exactly the same issue as OP when switching to Jellyfin and the only thing that fixed it was using the tvdb extension.
Yeah and setting it in library settings
Thanks...tvdb extension is indeed installed. Seems the issue derived from the .nfo files having still old crap from S01. That, and the episodes had S02 naming on it, even being the "first" season of Bly Manor. So that messed with Jellyfin...I think it got it correctly identified now, using different folders for each show. But now Sonarr can't find it, as it wants a single show and folder for both of these :(