I have the exact same problem. After I rehabilitated my student loans, DOE created a second new account. So I asked them to remove the old account but they instead put both were permanently assigned to the government which then brought down my credit score over 60 points, right at the time I was looking to refinance my 13.9% car loan or trade it in for a better rate.
I logged into that website with my PIN and all the loans say "IN REPAYMENT". Where do I go from here? Thank you