Just to help anyone else who reads this in the future,
I didn’t have any luck replacing the midi file directly on the disk. If I changed the midi file directly on the disk, it would still play the original midi file I used when I exported the song via UTOOL. I could only update the MIDI by exporting it again, pointing to the updated MIDI file I wanted to use. I assume it must embed that midi file into the song.dat file, perhaps?