To be honest, this is all pretty much normal, give or take on some of the circumstances.
The doe (especially if a first time mother) will usually kill and sometimes devour her young simply because she is inexperienced, senses that perhaps the young are sick or unsafe and will not survive, or feels that she is unable to care for them because she may not be healthy unough. There are many, many contributing factors to this that we as humans may not see, so try not to fret about it and hold it against her.
It's alright if the young are burried deep in their nest. Rabbits will dig, and the deeper they go, the safer they feel. This goes for both adults and young. Some times does will burry their young in unusually deep nests because they may feel that they aren't protected or warm enough. As long as the young are being fed and kept warm, they should be fine. You should replace the cedar shavings (these are lethal to young rabbits because of the phenols) and any excrements in the nest to prevent bacteria and diseases. This is also normal for the doe to deficate in the nest, so just be sure to keep it clean.
Most importantly that you must know, is that does will always appear to be neglecting their young. They only feed them either at night or early morning and they usually only do this once a day for a few minutes.The rest of thetimethey will ignore the young. This is perfectly normal, and this is what a doe should do.
It is also normal to see scratch marks on the young as well. This usually means that the mother simply needs to have her nails trimmed. Unless she is actually shredding her young to pieces, then she isn't doing this intentionally.
If the young have lasted a few days after birth, then the mother is taking care of them. Generally, if the mother has neglected them, they will die within 3 days due to lack of food. It's also normal to have a few runts die. This isn't because they aren't getting enough food or the mother has chosen to neglect only certain kits, it's because they are runt. They aren't physically ment to live a long time.
I very strongly suggest that you put the kits back in the nest with their mother. Taking them away and bottle feeding them will alter their highly sensitive digestive system that was originally adapted to the mother's milk. Giving them bottled milk should only be used in dire situations. Bottled milk does not have all the same nutrients and antibodies found in natural milk whichis extremely essential in a young rabbits first few weeks of development.
So in all, your rabbit is acting normal and doing what comes naturally to her and her young. Please try to refrain from stressing about all the minor issues which are perfectly understandable but again, there is no need tofear.
As long as the babies are being fed by the mother, and you keep the nest clean, everything will be fine.
Hope this helps.
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Otherwise it can be harmful to the babies in the form of diseases, etc. The cedar chips should also be replaced with some other type of bedding - such as kiln dried pine chips. 
