Music Scanner scrambles and omits tracks on Multi-CD sets

These tell us that the artist and the album has indeed been matched with the last.fm agent.
So this library will fall into disrepair more and more in the coming years, I’m afraid.

If your server is up to it, you could create a second music library, which you are pointing to the very same folders. But you select ‘Plex Music’ for both Agent and Scanner.
And activate ‘Prefer local metadata’ as well.

Scanning this may take very long time (with the size of your collection it make take days).
But if you let it proceed as long as it takes (don’t interfere too early and correct any mistakes manually) you’ll have a library which you can use to compare how the old and the new code behave.

You need to keep in mind that this will enlarge your database and the Plex data folder considerably. So only try it if your server has plenty of resources.