Episodes showing multiple times in different seasons

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Is metadata the only thing you're changing? Are they still organized in the file system the same way? That may be part of the issue.

The only other thing I can say is that when you edit the metadata, you likely need to clear out just about everything, as some fields will override any changes you make (e.g., I know IMDb ID can sometimes be problematic when trying to shift a series from a wrong series identification).