Hi,
First we agree that MB5S report is working exactly as required. This SAP standard behavior. Secondly, MR11 is different from MB5S, this you also know.
As you mention these PO belongs to old data - changes shows impacts on current business values also (possible). Deleting/reversing all subsequent documents to cancel freight conditions also not suggestible.
Instruct user to check MR11 to check quantity wise differences and MB5S for qty and value wise differences.