If you select this option in the DZ Report Options window then balancing adjustments will be made to the resulting report. The report total taxable and total exempt amounts will be made meaningful - in that they will agree with the sales documents included in the report. If you do not select this option, then the balancing adjustments will not be made. With either selection, the total sales tax amount will be the same, unless tax detail records are missing from the transaction history.
We have a sales document that includes a single taxable item priced at $1,000. Let's assume that this item is subject to a city tax, a county tax, and a state tax. Each of those three taxes will show an amount taxable of $1,000. Without the balancing adjustment, the report will add those lines up to show a total amount taxable of $3,000 ($1,000 for each of the three tax details). With the balancing adjustment, the report will show a total amount taxable of $1,000.
The simplest way to see what effect the reconcile documents selection has on a report is to generate a report that contains only one document. For example, restrict the report to a single document number. If you are running a non-optimized report, then be sure to also restrict the report to the date of the document (Or else the report may take an excessive amount of time to generate). Run this report with Reconcile Documents selected, and then rerun it with the Reconcile documents option cleared. Compare the two reports. If the document that you chose does not require a reconciling adjustment, then the two reports will be identical. If the document does require a reconciling adjustment, then you should be able to see and understand the purpose of the adjustment. You should select both the Detailed Report and the Print Report Body options (You must expand on the Primary Sort Order to see the Print Report Body checkbox).