As for EEPROM, have you heard anybody doing without special tool - IE reading chip and using hex editor to re-code and re-write?
It might be just a connection issue try to swap those two working boards to a non-working one and then make sure it is connected properly.
If it doesn't work then make sure to check the logs it should tell you the issue as to why one of the hashboard is not detected.
The easiest solution for the mix board is by using other firmware like Braiins or Vnish as mentioned above.