To explain where I went wrong: in the save file, you have characters defined with their attack/health levels (the number of HP up / POW up items each one collected), and implicitly if a character is defined in there, we assume they are unlocked. Foolishly, I kept TGO-03 defined in the basic save file, and so she was unlocked from the start.
As well, I never implemented deleting the save file lmfao
