Well, maybe it's just the way I'd approach the task. If the fretboard's coming off, then going back down, I would pull the frets first. Once glued back, I would replane the fingerboard flat (all that heat can do funky things), then replace the frets. That may not be standard procedure, but the way I would approach it. So pulling them to rout the f/b seemed like a non-issue to me. It sounds like you envision keeping the frets in place while pulling to board and then regluing? You are a better workman than am I!
As for hitting the rod, if the router is set at 2 hairs shy of the bottom of the board, so that it doesn't cut all the way through, then finishing up the groove by hand would present no danger. To me, it sounds like the rod is shot anyway, and the router bit is not that precious--so that if it were accidentally hit, I wouldn't worry. But that's a Texan for ya.
Tell you guys what--forget the whole idea.
All I was trying to do was save Paul some finish work.
Oooh--Paul, an even better idea-- come in from the back of the neck and pull that rod out. Cover over the resultant groove w/ a skunk stripe a la Fender. You've then got some finish work to do, but no fretboard yanking.
