Hi chris
Well tax credits and taxes are treated complelety differently, so the overpayment will be recovered and the underpayment from the BR code will be repaid to her, this is pending she has no tax that might owed from any other years first.
does she still received child or working tax credit? if so then you may find that they are already collecting the amount she owes tax credits through her current payments.
its not my job to apolgise for the state of the post status with the tax office, but i can offer an explaination. a new computer system was introduced in june, meaning the old one had to shut down and the records needed to be transferred across to the new one, this meant the post (which was already 2/3 weeks behind) then built up, leading to a larger backlog.
hope the advice helps
Laney