There isn't a way to fully get it back to factory defaults except by sending it a Sysex message from a computer.
However, if you're only looking to fix a communication issue, you can hold Audio Loop 1 as you power up the RG-16. Once the lights flash, release Audio Loop 1. The only light that should be on (aside from the Power LED) is Function Switch 3. If any others are on, press the corresponding button to turn them off. Once you're done, press Write on the RG-16. That should do it.