In light of these problems with the Downloads functionality and other problems I also had in the past with movies that have multiple versions, I decided to “split apart” all the movies in my library.
It’s not great, but at least it makes the Downloads functionality work without errors and without unexpected transcoding. I can now also download the exact version I want.
But there are two inconveniences with this solution:
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My library is now full of duplicated movie entries.
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The split functionality doesn’t work with extras when both movie files are in the same folder. The extras just aren’t detected at all after the split. So for all the movies with extras I needed to split, I had to put one of the movie files in its own separate folder, along with a second copy of all the extras. So this solution is taking more storage than before.
@BigWheel and @anon18523487, thanks for your help. If you need further information to help investigate and solve the problems highlighted in this thread, please don’t hesitate to ask.
I would also like to stress how important and how badly needed a better way to manage multiple versions of the same movie is in Plex. And such a solution would need to also take the Downloads and movie extras functionalities into account. I really hope this is something that has a high priority for future development.