What do you mean? That never happens. If the file is named S03E01 it will be in Season 3 no matter what Order you have set, If you have set Absolute Order then it will have No Metadata, If you have DVD Order it will have the data from DVD Ordering, if you have Aired Order it will have the data from that order. Plex has NO way of moving episodes to places different from what the file is named as.
But the episode on TVdb being assigned to different seasons depending on the ordering is exactly like the OP is wanting. Now you might run into the problem of having S01E13 in Absolute Order being the same as S00E01 in Aired Order but I don’t see how that would be a problem except for things like Trakt Sync because it would mark the episode as watched if 1 was watched & the other wasn’t, but that’s an unsupported use case so it shouldn’t matter. If the Watchlist updated from plays on the server it could be a problem too, but it doesn’t either, so, again, not a problem.
The best solution would be to fix this on TVdb because it sounds like TVdb has a problem that nobody has fixed yet. You can do it with a free account. I used to do this stuff a lot on TVdb until I had some bad experiences with their mods & removed all my contributions
But even still I think this would be a great benefit. I still think the Episode ID Matching suggestion solves this better, but it seems like a simple thing to implement
