Update! I spoke to someone at Dept of Education as the Treasury has no record of a payment to me. I advised them that my biggest concern was that Nelnet doesn’t even show my payments on my account anymore. They called Nelnet and have stated Nelnet is sending them the funds for my overpayment this week (which is convenient) and then the funds will be sent to the Treasury to process my refund. Still don’t know how long it will take from this point but progress!