A new Sonic collection is rumored to come out in June. Will include a majority of classic games and also games that haven't been in circulation for years. Won't include Sonic 3.
Fuck sake! If this is an issue with the Michael Jackson music then just get somebody to create a new soundtrack.
The Sonic 3 & Knuckles PC collection from the 90s already had a separate soundtrack, the original soundtrack from before MJ and his team were brought on. And I'm sure there are plenty of artists at Sega who would love to make new music for S3&K.
It's not as easy as flipping a switch and changing the music or Sega would've already done that. Back in 2011 was the last time Sega released S3&K. A year later in 2012 Cirocco Jones, and Bobby Brooks seemed to confirm some sort of plausible lawsuit going on behind scenes. It seems Sega owes unpaid royalties for the music. I'd bet that is the reason we don't see any new ports, not so much the MJ issue unless his estate is also owed money.
Sega has likely been dodging the issue of owed royalties, and lawsuits by not releasing the game again. If they changed the tracks that would likely be seen as further evidence of the artists not being payed properly, and just digging their hole deeper. That's my theory from those old comments and how we have never seen the game since then, even though they already have a complete in house soundtrack for the game.