eter@Elite8200:~/7i90$ sudo mesaflash --device 7i90hd --epp --write 7i90_epp_sv4_7i47s.bit
Checking file... OK
  File type: Xilinx bit file
Error: BootSector is invalid
peter@Elite8200:~/7i90$ sudo mesaflash --device 7i90hd --epp --write 7i90_epp_sv4_7i47s.bit --fix-boot-block
Checking file... OK
  File type: Xilinx bit file
Erasing sector 0 for boot block
BootBlock installed
FLASH memory sectors to write: 6, max sectors in area: 16
Erasing FLASH memory sectors starting from 0x100000...
  |EEEEEE
Programming FLASH memory sectors starting from 0x100000...
  |WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW
Board configuration updated successfully.
Checking file... OK
  File type: Xilinx bit file
Boot sector OK
Verifying FLASH memory sectors starting from 0x100000...
  |VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV
Board FLASH memory verified successfully.

You must power cycle the hardware
peter@Elite8200:~/7i90$