Oh that’s interesting I’ll have to look into this.
Re-flashing the FT2232 won’t void your warranty but it might cause the Alchitry Loader to stop recognizing it unless you flash it back to the defaults.
EDIT: I just tried it out and you can make it work with both Vivado and Alchitry Labs.
./program_ftdi -write -f FT2232H -v "Alchitry" -b "Alchitry Au" -d "Alchitry Au" -s 000000
Use “Alchitry Au+” if you have an Au+. The serial number isn’t used by Alchitry Labs so you can set it to anything.