We have seen this error as well in Notes 6.5.5 mail files too. I have never found the exact cause, but it seems that “deleted” documents or deletion stubs are being included somehow in the collection of documents created by the archive now selection criteria. Then when the archive process trys to copy the document in question it fails with this error and quits.
Users are still able to use Archive Selected Documents without seeing this error.
Our work-around is to run fixup and compact on the mail file and also make sure that the Trash is emptied (so no soft deletes are still present).
If the user can create a new local replica of the file with the error they may be able to archive now from that new replica. This works because the replicator will not copy the “broken document(s)”.