You can vacuum AS and rescape with it without problems. I do both of these with the AS I've had for nearly a year, and it hasn't caused any issues at all. Just make sure your gravel vac isn't so strong that it will suck up the AS.
Disturbing the substrate will cloud the water temporarily, but it doesn't seem to affect anything negatively.
When I do any rescaping, I go with a 50% water change, as is the weekly schedule anyway. When doing half the tank or more, I will go with two straight 50% WC's back to back. I've never had an issue with fish health or algae blooms this way.