Can I re-do FPS from two months ago? Er NI was deducted in error, we refunded to employee and was deducted off next PAYE payment as told by HMRC, but shows o/s on HMRC?

When called HMRC they said to refund employee on next pay run and deduct the amount from PAYE payment and they would work it out from there, they never said I had to re-submit FPS but it's now an amount outstanding on our account and they're charging interest? The employee this is in ref to is the last month being paid as leaving so want to get this corrected.