Make sure you have firmware.exe in your commands folder, and copy across the latest available eeprom image file ("default.bin" from the folder development_files/(your board model)/eeprom) to your SD card. In FLOS, enter:

FIRMWARE default.bin 0

This updates slot 0 (which holds the EEPROM-based copy of the OS and bootcode), plus SLOTS 1 and 2.

For incremental updates it is best to use EEPROM.EXE as the image files provided for Firmware.exe are only updated when absolutely necessary (EEPROM.EXE is safer and more elegant too).