In QuickBooks 2010, you should not use A/P to apply credits to Bills. Instead, use a Bank account. This problem is fixed in QuickBooks 2012.

NOTE: Take care of your data and company file. You must perform steps 1 and 2 below before proceeding.

1. Before any fixes are done - Make a backup of the file.
2. Before any fixes are done - Run the following reports for all dates and print them off. (This is the base line of transactions as they exist now)
   1. Balance Sheet and Trial Balance
   2. Aging and Supplier Balance Summary reports
       
3. Go to Advanced Find (Edit/Find/Advanced tab), select the following, then click Find:
   1. Transaction Type = Cheque
   2. Account = Accounts Payable
   3. Name = (Supplier with the problem)
       
4. Select the first Cheque, then click Go To.
5. Change the Accounts Payable account line to be a new Bank account. (This will break the links between the bills and credits.)
6. Go to Pay Bills, change the Bank account to the new Bank account …
   
   a)    Change the date, and repay the Bills and
   b)    Pay only the amount that is in the bank account;
    
7. Return to Advanced Find, and select the next Cheque - Repeat steps 4 and 5 until each Cheque has been used to Pay Bills.
8. Return to Advanced Find, and change the Name to the next Supplier with a problem.
9. Work through each Cheque, for each Supplier with this problem, until there are no more Cheques to accounts payable
10. Once all fixes are done - Run the Vat 100 report for all dates and print it off AGAIN (This report should now be accurate)
11. If the differences are not too great, you can file correctly with the next filing period. If they are great you may want to speak to your Accountant or HMRC.