Github and credential-osxkeychain delete access
Yes, git-credential-osxkeychain can delete the GitHub entry in your KeyChain. It will do that when it gets a failed authentication, I've had it happen to me.

I'm not sure it's a good idea, but I understand the reason. It has the access to do it and it's not like it serves any purpose any more. 

GitHub can't do it from their end, they don't have the permissions over your KeyChain.