Use small diameter tubing (e.g., airline) to siphon water back into the tank if you're worried, or do the refill in stages. Fry are tough, never had a problem myself.
I've never had a problem either, I use the gravel vac like I would any time, except I'm more vigilant. If a few fry do get sucked up, I quickly scoop them up and put them back in the tank, unless the fry are super tiny, I wouldn't worry too much.
Man shortly after the fry hatched the male killed the female. I think the male ate some of the fry before I took him out an moved him into another tank.