Duplicates when moving files

[TheDreadPirate]

If you have folders in place, Jellyfin will create empty shows/seasons/movies, etc., even if there aren't any files in them.

IMO, what you should do is create a separate "Work in progress" library for this scenario. What you're describing is, I think, the expected behavior. Even if it is undesired. But what you're doing is atypical for movies. For shows there is a library option to merge shows when they are spread across drives that a movies library lacks.