Could you create an anti-patch? If the data is always going to be in the same place (ie - it will always be at 36/010A), then you could make your manual edits, create a patch with just the music tracks change, and then re-apply that patch to your rom after every time you save in Temporal Flux. I had to do that with my FFVI hack, because FF3usME kept trying to overwrite some of my relocated data. I created an anti-patch to put the minimap back where I intended it to be, and ran that anti-patch after every save.
I completed the music expansion hack, and as long as I was relocating data, I expanded the tables to allow for up to 101 music tracks (hex: $65). I will start a new thread for the actual patch.