In this case, don't create a paycheck.
Instead, create a regular check for the net pay amount. In the detail area of the check, use the same bank account you're writing the check from. This will create both a debit and credit to your bank account, for a net 0.00 change in the account. Print the check with a new check number and give it to the employee as a replacement.
Then, when you reconcile, clear both the old check, the new one (when it clears) and the "deposit" you'll see in reconcile that is the result of using the bank account in the detail area of the check.
