I would move it to a towel. Most hatching floors have wire mesh that can easily break the yolk sac. You can push it back in yourself. I don't grow nails well, so my fingertips are blunt. Push the yolk sac straight in with one of your fingertips. You won't make progress when they peep.. the pressure of them peeping pushes it back out. Once you get it worked in hold your finger against their naval for about an hour.. if they peep before the naval seals, the yolk sac will pop back out. The naval will seal with the yolk sac on the inside if you keep some pressure on their naval. I've done this a few times now and all survived. I wrap the chick in a dry washcloth, for warmth, and just turn on a movie to pass the time.
If you have more with 'rough navals' you may want to lower the humidity a little bit. It means the humidity was too high during incubation so the yolk sac is too big for them to absorb.