Solved. The problem turned out to be much more simple than I realized. Simply, when I killed the booting main.py with CTRL-C, one of my files was not closing. Since this coding bug was run at boot, it meant no matter what I did the file would always be held open by a killed process.
If you get a 7001 EPERM error, verify you don't have a file object open to it (unintentially)