SOLVED: Missing files

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Jellyfin expects a certain layout that you're getting close to, but not abiding by: https://jellyfin.org/docs/general/server/media/movies/.

You have two options. One is for psychopaths: everything in a single folder. The other is one folder for each film, but it needs to share the name of the film, e.g., Harry Potter and the Philosopher's Stone (2001). The two examples you attached are Collection > Movie.mkv which will lead to unexpected results, as you've seen. Organize them as described in the documentation and you'll have better luck.

Movies (Root Folder) >
|
| > Harry Potter and the Philosopher's Stone (2001) > Harry Potter and the Philosopher's Stone (2001).mkv
| > Harry Potter and the Deathly Hallows Part 1 (2010) > Harry Potter and the Deathly Hallows Part 1 (2010).mkv
| > Harry Potter and the Deathly Hallows Part 2 (2011) > Harry Potter and the Deathly Hallows Part 1 (2011).mkv