As long as they can get through cleanly, yes. I have a chain link fence separating the halves of my run and find that chicks up to around 6, 7 weeks can squirt under. But once they no longer fit so easily, I kick a lot more litter under there to discourage them from trying to use that as a...
Nice. Are you sure the little ones can't squirt out through the openings in the separator fence? (I have the same temporary fencing behind the house, but it's hot and I don't want to go out and measure it!)
Plan on 1-2 weeks see but no touch. Time it takes really depends on your adult flock...