Currently if the document has been deleted from mail file (may be calendar invitation or mail), then we cannot determine who deleted it and why ? User actions are not tracked. Even if server purges that document then server doesn't log why the document was purged and who has given instructions to purge document. Further there is no recovery process of such purged/deleted document. There is a feature request to provide a view where one can easily check the purged/deleted documents by server/user and put them in temporary bin from where they can be recovered. So lot of issues related to questionable deletions/purging can be addressed with such feature.
Even in Domino 10, it logs the deletions but that will just give the ID of user who deleted document. If user has accidentally deleted the document then there is no way to convince the user about how the document was deleted. Further many custom scripts/apps uses User ID to perform various actions, so that doesn't necessarily mean user has deleted the document.