There are a few ways to handle this:
- Void the payments in Payables (assuming these are payables checks). Make sure to use a current void date, you don't want to have these create 2008 transactions! This would make the payables invoices now open, so you would need to clean that up. You can either void these as well, again using current void dates, or create a credit memo to apply to them to clear them out. If you void the invoices, you will reverse the GL distributions they originally had and you may need to make GL adjustments to those. If you create a credit memo, you can determine what GL account to use.
- Enter a bank increase adjustment for the checks you want to clear. For example, let's say there are 5 checks for a total of $3,000. You can enter one bank increase adjustment for $3,000. The debit will be cash, you will need to decide what account to use for the credit. Once posted, on your next bank reconciliation you can select the 5 checks you want to clear and your $3,000 adjustment and they will net out to a zero difference.