This may not be the easiest solution but it worked for me.
In order to meet a deadline I filed the VAT return from HMRC, and forgot to file on QBO. Ended up with an exception report which was not included in the HMRC filed figures. The subsequent payment in the bank account (taken by HMRC) was different to the amount filed and waiting to be paid on QBO.
(If you have posted an incorrect payment as well, start by finding the cheque payment (search by amount) and delete this).
When a VAT return is filed on QBO it creates a journal entry dated to VAT period end. In this instance it was a VAT quarter. This journal is - DR Vat control; CR VAT Suspense. This journal can be located by viewing all transactions in VAT Suspense. QBO will not allow any sort of amendment to this journal.
However, it will allow you to add an additional journal for the period/quarter. Therefore, post a journal to either DR or CR VAT Control with the balancing entry going to VAT Suspense, representing the difference between filed amount to HMRC and filed amount on QBO.
VAT suspense balance should now equal the HMRC filed amount.
Then, manually post a payment to the bank account (via cheques) to VAT Suspense. The balance on VAT suspense should now be zero.
Go to VAT History and click VAT return as paid. This is purely cosmetic and the amount showing on the screen will still be incorrect, and a 0.00 payment will show, but the balance sheet will be correct. Just keep details with your VAT return of what happened.
In the following VAT period/quarter a manual adjustment will be need to correct that return for the entries that were not included in the previous return.
If you need to print historic VAT reports, view on screen then use CTRL P.