Yeah, flashrec backs up your original recovery menu to the SD card and then replaces it with amon ra. You don't really need the original one any more, so that's not an issue.
To clear things up, your radio and your firmware are separate things, so a nandroid backup/restore won't affect your radio in any way. There's no backup/restore option for the radio, so all you can do is flash them again.
Be warned though, if you do screw up flashing the radio it could brick your phone. Luckily there's not much to go wrong, other than loosing power. So, do not remove the battery whilst flashing a radio. No matter what the phone does.