You’ve identified the arch nemesis of the faneditor……. Music.
If you haven’t been able to remove the music using 6 channel isolation and standard noise reduction software, then you’re a bit stuck.
If the remaining music is very quiet you can sometimes add the new score over the top which drowns out the old score.
Beyond that the only option really is to rebuild the audio track from scratch. It’s painstaking but achievable for sound effects, and virtually impossible for dialogue.