QuickBooks -Invoice Basis to Cash Basis Vat Return

I have a new client on QB’s. They had never used the vat module to submit vat returns but I have sorted the set-up of this out now (for EC sales/purchases etc) and last quarter to 31 October I submitted the vat through the QB package using the accruals/invoice basis and all was fine. I have changed their vat quarters to calendar quarters to tie up with their year-end and so the return now due is for the 2 months of Nov and Dec. From 1 Nov I have changed them to the cash basis for vat (they often have a 2 month wait between invoice and payment) by going into the HMRC supplier account and changing the vat set up from accruals to cash. (It took me a while to find how this was done as most answers online just talk about changing reports between accruals and cash basis….which is just on the customise reports button.)

When I run a cash basis vat report for the two months it has the obvious overlaps with last period. These are all fine and I have been through line by line and know what to adjust to cancel any double counts in changing from an accrual to a cash basis. However, the report also has huge brought forward amounts which add into the vat balances. These b/f amounts are usually “Exception” report amounts from a previous period. I know they should be clear this period except for one or two small items. If I run the vat report for the last quarter on a cash basis, I get exactly these “Exception” figures. So for some reason QB is calculating last quarter on a cash basis and adding them into my vat return this time.  (Checking the vat report on an accruals basis it ties exactly with the B/S so that is all fine.)

What is the best way to correct these “Exception” amounts? Adjustments to the vat return figures in QB appear to get journaled to the B/S. There does not seem to be a way of just taking these figures out. I have phoned QB and they did not seem to understand the question. I would have thought it was not an uncommon situation.  Has anyone had a similar problem and how did you correct it? In the mean time I will back up and have a go at fixing it myself. I mainly use Sage and these type of changes don’t seem to give such big problems.

I would be very grateful if anyone could point me in the right direction. I would like to keep using the QB vat module to submit returns, but if I can’t fix it then I will have to revert to filing through HMRC login.

Thank you.