Yes, it is OK to remove top rails with the pool full. This is assuming that the pool is level and round. I would go a few at a time as you work around the pool.

When you pull the first rail you will have a little separation. Normally a couple of strong people can push the rail back into place while another person shoots in the screws with a screw gun.

If you are doing multiple rails, like is your case, just note the amount of separation and try to make it up by setting some of the rails in a little wider hole pattern. If you keep all your uprights straight up and down, you will be fine when you get back around to where you started.

Dennis