<A target="_blank" href="http://www-01.ibm.com/support/docview.wss?uid=swg21368251">It seems that, under Notes/Domino 8.0.2 and 8.5</A>, if you delete a folder in your active mailfile, that deletion will be "replicated" to an archive copy of the mailfile. The individual messages will not be deleted. This Technote includes a link to the fix.