Roon Core Machine
Do you have your FLAC files stored in a different location than the Apple Music files? If so, just add that location as a watched folder and make sure the music files you don’t want are not in there. If you need assistance with this, can you share a screenshot of Settings > Storage?
Also, make sure that the ‘Music Folder’ is disabled (assuming that this is not the folder where you store your FLAC files).
It’s been a while since you let us know of your preference when it comes to your music library. I wonder, did the suggestions shared on this thread help? Can we do anything else for you ?