tldr: There is no way to change/refund an EIP payment if the rep credits the wrong phone. Be careful when trusting the tmobile rep is doing the credit correctly. It could end up costing you hundreds of dollars as in this case.
I went in store to pay off some of the money I owed on the EIP for 2 of my phones. The in store rep ended up applying the payment to the wrong phones, applying them to phones that I am receiving monthly credits for instead.
After realizing their mistake, I attempted to get the payments moved to the correct phones. Both in store reps and Customer Care reps said there is no way in their system to reverse the payment and apply it to the correct phone. I was advised to attempt a chargeback through my bank to get the payments reversed, then attempting to pay on the phones again.
Needless to say, because these payments were applied to the wrong phones, shortening the months remaining on phones I am receiving credits for, I am losing HUNDREDS of dollars in credits on those phones. It's disappointing that refunding EIP payments isn't something their system supports.