Yahama FS1R Firmware Update Notes:

When updating the FS1R to a new firmware, the J1 jumper needs to be closed during the first power up with the new EPROM in place. After the first power up, the CPU will be flashed with the new code. Once this is done and the FS1R is powered down, the jumper can be returned to its normal open position and the FS1R can again be booted normally with the new EPROM.

This is a very unorthodox procedure as far as firmware updates go, and is not mentioned even within Yahaha's published service manual.