If the bootloader is corrupt, and it does happen from time to time. You’ll need to write a new bootloader to the Rainbowduino.
From memory the Rainbowduino uses the Arduino NG Nano bootloader - but any NG should be fine.
You’ll either need a STK500 programmer (or clone) or you could use a Seeeduino to program the Raindbowduino through UART.