My suggestion would be to remove the turner, lay them down and hand turn the ones that still need to be turned. The turners can cause safety issues if they are the original turners that turn the eggs sitting upright. Eggs don't need to be turned after 2 weeks so any that are that far along I wouldn't worry about. Staggered hatches in one incubator can be hard because of the humidity needs. If you are constantly having to have humidity up for hatchers the earlier eggs are going to possibily not loose enough moisture. A lot depends on how far apart your sets of eggs are.
The other thing you can do, is some of the turners are made so that you can take the racks out. If your turner has detatchable racks you can take the racks out from the eggs that are going to go into lockdown and leave the others in the turner. Not a big recommendation from me, because like I said, it's safer with the turners out, but it's been done.