The Comfort module has nothing to do with the Immobiizer system on your car, so it will be driveable. The Remote keys will have to be reprogrammed, which most times requires a VAG-Com to perform, though the 2 key method is an option as well. In my experience though, most times the 2 key method doesn't work, and you have to clear the learned values out of the module with the VAG-Com and program them that way.
You don't have to disconnect the battery. To reprogram the keys with a VAG-Com, go to address word 46, function 10, channel 0. This will delete the learned values stored in the control module. After deleting the learned values, go to Function 10, channel 1, and enter the amount of keys you want to program. After saving that value, push the same button on all remotes one at a time until you hear the horn beep, which confirms the remote has been stored in the system.