Brian/Andrew:
In the 1990's, using ACCPAC Plus as a Controller, we reconciled Sales Analysis to Ledger every month. The only time it failed was when someone changed the period number assigned to the transaction to create a mismatch between the date and assigned fiscal period. I see no reason why this shouldn't continue to work today. Users were not allowed to edit data, I can see where this would be a problem.
Brian states that the Credit Note is changing the Invoice date, not the Set paid indicator as Andrew mentions. If Brian's concern is valid then there is a bug. It shouldn't be too difficult for Softrak to test this to see if it can be duplicated.