I made removable nest boxes for easy cleaning, but I've had to keep them out altogether because that's where my chicks want to sleep.  I tried lowering the sides and then covering them up but they still wanting to sleep on top.  Of course, now that they are removed, the chicks STILL sleep in the spot where the nest boxes were.  I put portable roosts there, in hopes that they will grow to like their roosts and when the roosts can be moved to the appropriate sleeping location, the chicks will follow.  Fingers crossed!