My condo has an opening in the top and bottom (easy to do if you have a NIC condo with zipties - I just secure the top with binder clips) so when I put Lola back in her condo the first week or two for bed I'd put her back in the top story and she got used to it.
Buns are creatures of habit - there have been several time where I've needed to clean a shelf in her condo and pulled it out and she's hopped up on an invisible shelf and came crashing down even though it's CLEARLY not visible. Silly rabbit. Hopefully this is the case with your buns and they just don't realize yet that they have all this extra room.
