I imagine the stones would survive it, just fall out of the vanishing gauntlet. It’s not like the stones were a part of it, they were just being held in place by it, but then there’s the question of whether or not the contents of people’s pockets got snapped as well, we know the pager Fury had didn’t count as “part of him”.

And no, they used the ant man tech to go back in time, no stones there.