Disc 1 shows up as
1 1999
1 1999
2 Little Red Corvette
2 Little Red Corvette
3 Delirious
3 Delirious
… and so on. The other discs, since they only exist for the super deluxe edition, are fine in that regard.
The files are in separate folders, and the ID3 tags for the super deluxe edition have the album title as “1999 (super deluxe edition)” other details (date, MusicBrainz IDs, etc.) which distinguish it from the “basic” edition, but despite several attempts at removing and re-adding the folder, Plex insists on merging them.
I’ve found these similar (closed) threads, but no resolutions yet:
I’m happy to provide additional information that may help.
Plex Web Version 4.100.1
PMS Version 1.31.2.6810 on Ubuntu 22.04.2 LTS