Mesaflash version 3.4.9
Configuration and diagnostic tool for Mesa Electronics PCI(E)/ETH/EPP/USB/SPI boards
Try 'mesaflash --help' for more information
jeff@LinuxCNC-Lathe:~$ mesaflash --device 7I96s --addr 10.10.10.10 --write 7i96s_p1encd.bin
Can't find bitfile 7i96s_p1encd.bin
jeff@LinuxCNC-Lathe:~$ mesaflash --device 7I96s --addr 10.10.10.10 --write 7i96s_p1encd.bin
Checking file... OK
  File type: Efinix bin file
FLASH memory sectors to write: 11, max sectors in area: 16
Erasing FLASH memory sectors starting from 0x100000...
  |EEEEEEEEEEE
Programming FLASH memory sectors starting from 0x100000...
  |WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW
Board configuration updated successfully.
Checking file... OK
  File type: Efinix bin file
Verifying FLASH memory sectors starting from 0x100000...
  |VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV
Board FLASH memory verified successfully.

You must power cycle the hardware or use the --reload command to load a new firmware.
jeff@LinuxCNC-Lathe:~$ mesaflash --device 7I96s --addr 10.10.10.10  --reload
jeff@LinuxCNC-Lathe:~$ ^C
jeff@LinuxCNC-Lathe:~$