I honestly don’t know if it’ll properly load upgrades that are within the same file as the source, as I’ve never wanted to tamper with them, but you may just be better off merging the two .mid files together in REAPER, re-exporting them, and updating the songs.dta file in the original package.
You are about to leave Rhythm Gaming World and access the external songs DB. While no song or file sold for commercially available videogames is hosted there and only fan generated content is allowed, Rhythm Gaming World has no direct control over the database and no files are hosted here. Alright, we had to made you aware of this, now you can visit the database!