I'm sorry! This is a problem many pet owners encounter- accidental litters. Litters are a big deal for first timers.
Keep in mind- she had to play an active part in the breeding. She must have known what she was getting into, so please don't feel too bad. When the babies start venturing outside of the nest, STOP feeding anything wet of any kind. Dead babies are no fun.Otherwise, your and Timmy both are doing great jobs.
Everything is going well, I am trying to load up some pics asap, but time is of big concern when you have dial up and 12 rabbits! I just got 2 new ones today and its all wonderful but a lot of hard work. The kits are so fat and warm and snuggly, they are so well cared for, they have the best Mum, and the best Mum's Mum too
Their nest is cosy and compact and I check on them 3 times overnight every night. They are huge already.
I wouldn't disturb them too much, since you have already ascertained that they are alive and well fed, I wouldn't check them more than once in 24 hours. If mom gets nervous about all the interruptions, she might hurt the babies.