Sales tax collected discrepancies

We have recently noticed a negative amount (overpayment) on our Sales Tax Payable general account. We have been submitting sales tax based on the "sales tax collected" amount in the Sales Tax Summary Report.

We have had large projects going thru SAGE 100 in the recent years. These types of big projects always involve down payment, prior-to-ship payment, and the final payment stretching across several months/years.

Several project invoices have been credited and re-billed as customers claim tax-exemption after the first invoice posted in the previous month/year.

We are not sure if the system is calculating “sales taxes collected” correctly on all these project invoices.  Is the "sales tax collected" correct when you have credit and rebill? How do we reconcile the "recap" numbers in the "sales tax collected" in the Sales Tax Summary Report?