The GPU lives!
I looked up how atiflash.exe worked and discovered a (quite serious) flaw in the .bat files: They both flashed to GPU 0!
This meant that first, I would correctly flash the master BIOS to GPU 0 (the master GPU), but after that I would immediately overwrite it with the slave BIOS, while also leaving the slave BIOS at an older version.
Once I had changed slave.bat to write to GPU 1, it flashed correctly and my GPU is now running happily without CSM
Thanks for the help, I hope this will prevent future failed flashes.