Collections Based on Metadata Matching

[TheDreadPirate]

Regarding your collections being deleted, there is a Scheduled task that cleans up playlists and collections ON STARTUP when the associated media is not present.  You can disable this task.

Dashboard > Scheduled Tasks > Cleanup playlists and collections.  Click on it and delete the startup trigger.  Now Jellyfin SHOULDN'T remove collections or entries in collections automatically.

Jellyfin does create XMLs with the contents of your collections.  If you have a backup of the XML, you would simply need to restore the collection's folder(s), scan all libraries, and it will recreate the collections.  Including tags and whatnot.

Code:

<Item>
  <CollectionItems>
    <CollectionItem>
      <Path>/media/library/Movies/Batman Begins (2005) [tmdbid-272]/Batman Begins (2005) [tmdbid-272].mkv</Path>
    </CollectionItem>
    <CollectionItem>
      <Path>/media/library/Movies/The Dark Knight (2008) [tmdbid-155]/The Dark Knight (2008) [tmdbid-155].mkv</Path>
    </CollectionItem>
    <CollectionItem>
      <Path>/media/library/Movies/The Dark Knight Rises (2012) [tmdbid-49026]/The Dark Knight Rises (2012) [tmdbid-49026].mkv</Path>
    </CollectionItem>
  </CollectionItems>
</Item>

For docker, go to where you've mounted /config:
/config/data/collections

For baremetal Linux:
/var/lib/jellyfin/data/collections

If you're using MacOS on your mini, I don't know where the exact location would be.  But the collections folder would be in the same directory as the two Jellyfin database files.

Regarding the feature request at the end of your post.  I can't find anything about NFOs being used to define the contents of a collection, like we already do in XML format.  Only that there are tags you can add to movie NFOs to specify a collection they belong in.