Music Scanner scrambles and omits tracks on Multi-CD sets

Verify the presence of ‘Album Artist’ meta tags. These are very important in Plex.

The folder organization and the ‘Album Artist’ are intertwined.
As mentioned already, all albums must be in a stored in a folder structure of
Music > Artist > Album > Tracks

Now imagine a bunch of albums stored inside a certain album artist folder.
If only one of these albums has a deviant album artist in its metatags, the whole artist and its albums may get renamed to the deviant artist name.

If you can guarantee that this is not the case for any of your albums, then enable “Prefer local metadata” – before starting the first library scan.

(Now this may seem unlikely to you, but consider albums which were made as a collaboration. Or think of “sampler” and soundtrack albums. These are handled as a regular artist in Plex [with the name Various Artists], so these too must follow the folder structure.)