JP1 Remotes

If after making updates to your remote (in my case URC 9910), is it possible to go back to the factory settings if you get it messed up?

Yes. The factory settings are in ROM, which cannot be touched by JP1. All the upgrades are in eeprom and override ROM contents where they correspond, but you can always delete part or all of what was in eeprom to reenable anything in ROM that was hidden by those eeprom contents.