phil@bport:~/mesa/5i25/configs$ sudo  mesaflash --device 5i25 --write hostmot2/5i25_7i76x2.bit
[sudo] password for phil:
Checking file... OK
  File type: BIT file
Boot sector OK
EEPROM sectors to write: 6, max sectors in area: 16
Erasing EEPROM sectors starting from 0x100000...
  |EEEEEE
Programming EEPROM sectors starting from 0x100000...
  |WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW
Board configuration updated successfully.
Checking file... OK
  File type: BIT file
Boot sector OK
Verifying EEPROM sectors starting from 0x100000...
  |VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV
Board configuration verified successfully.

You must power cycle the hardware or use the --reload command to load a new firmware.
phil@bport:~/mesa/5i25/configs$ sudo  mesaflash --device 5i25 --reload
Waiting for FPGA configuration...OK