Seems like a subdirectory of a subdirectory issue. The naming conventions for movie libraries are as such:
The root folder would be MKVs in this case. If you didn't remove the other library, Jellyfin either a) doesn't like the naming convention used (e.g., the root folder not set as "MKVs") or b) already identified the movies in the other library.
Try removing the library that has the ISOs and add a new one where the root folder is the MKVs level. If your naming convention doesn't match the conventions (or come close to...some information may be unnecessary, but helps with identification of the movie) try more closely aligning with the recommendations in the documentation.
https://jellyfin.org/docs/general/server/media/movies/
Code:
Root Folder/
|
-- Movie Title (YYYY) [tmdb-id 1234]/
|
-- Movie Title (YYYY) [tmdb-id 1234].mkv
The root folder would be MKVs in this case. If you didn't remove the other library, Jellyfin either a) doesn't like the naming convention used (e.g., the root folder not set as "MKVs") or b) already identified the movies in the other library.
Try removing the library that has the ISOs and add a new one where the root folder is the MKVs level. If your naming convention doesn't match the conventions (or come close to...some information may be unnecessary, but helps with identification of the movie) try more closely aligning with the recommendations in the documentation.
https://jellyfin.org/docs/general/server/media/movies/
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