The Tax Summary and Tax Tracking reports in OE can be purged independantly, so there is no 100% guarantee that the amounts will be the same.

In the Tax Tracking file, credit note information is stored as negative, and the 'Doc Type' field gives a result of 'C' instead of 'I' for invoices. You shouldn't need to do anything special for summing transactions. You could put the Doc Type field onto your view to isolate the credit note details.

When was the last time you purged these reports? Years and years ago, there was a problem in the Tax Summary report where credit note information was saved as positive instead of negative. This has long since been fixed.