How Do I Clean Out The Nest Box?

Hi! I'm new to this forum and also very new to breeding budgies so I'm going to be asking a lot of questions on here. I thought I'd start with the most severe problem so far. How do I clean out the best box? The first baby is around 3 weeks now and the youngest is around 1or so and the best box has an odd smell around it. I'm not sure if that's normal or not but I'm just guessing it's not. I really want to clean it out but last time I tried the parents freaked out and started flying around everywhere and the babies started screaming. After that for a few minutes the hen seemed a little nervous about going into the best box but I'm not sure. Is there any way to clean it so the parents and the babies don't get scared? If not is it okay if they are scared? Will the parents stop caring for them if I clean it? Any help would be very much appreciated.