Sounds like she is wanting to move the pup to where she is comfortable whelping.
It doesn't sound like she's wanting to hurt the pup, just hide it.
If your whelping box is open a bit of cover on the top sometimes helps if they are nervous about having things or people around.
I have one that if I don't pen her in a x-pen in her box she will carry the pups to my bed when I'm not looking. LOL
It will be ok, remember to breathe...........
