George made a nice feature a long time ago : if a pit is open, there's always a visible ceiling under. So you don't need to manage ceilings in RTC editor, the engine does it for you.
I'm testing a wallset generated by my tool and the original ceiling bitmap is still displayed behind my new bitmap :

On the test map, I put cloned pits on the upper level and added cloned ceilings under each pit on the lower level. If I don't put these ceilings, the old bitmap is displayed.
The only way to solve this problem is to link the cloned pit object to the cloned ceiling object.