Ok, as we used to have a barn of around 50 show bunnies, I would like to offer some advice. First, ditch the cedar, use either kiln dried pine or aspen, or better yet towels or fleece. Cedar causes respiratory problems and could lead to URI's in the babies really quickly, especially within the confines of that stale environment within a rubbermaid container. Be prepared, they could already be compromised, which could be why mom started to reject them. It is unusual for a mom to start taking care of them and then stop. Handling them per se isn't bad, it is an old wives tale however, it could be stressing the doe and also causing her to reject them. What are their normal cages like? Ideally, the babies should have a nesting box with one slightly lowered side so mom can come and go and have some privacy. Her normal cage with a nesting box would probably be alot more relaxing for her. Rabbits like to be able to see, they are in fact a prey animal and I have found being unable to see around tends to make them stress over time.