Fantastic!! Glad you got it working.
I suspect that the changes were the reason for the failure of the git pull --recurse-submodles.
Git would have seen the changes to the drum.cpp file and made sure that it didn’t accidentally overwrite those (in case they were important). It’ll tell you what files are causing issues and you can just delete or rename which ever ones it mentions, and then it should work.
None of the individual .bin files are tracked on git (only the ones in the dist/ folder). So not sure why the one you had disappeared unless you ran make clean, or manually deleted the build folder.