[cypher]

I think you're probably right to clean more if it is that ammonia/pee smell, it's not good for them if it gets too much.
Can you find a pee spot or spots to just clean those areas more or it's just a general smell on everything?
Do they have a sand bath? Sometimes you can encourage them to pee in the sand by putting some of the smelly substrate in the sand.
It might be worth taking the risk & putting them in a larger cage if you have the space to keep both in different cages if they did fall out if all else fails.