To keep manual deletions add this bit of script to the QueryDocumentDelete and create a mail in database and record called "Deleted Entries." This will then mail any deletions that are made in the NAB. This does not work for deletions made via ADMINP but it works for every other type of deletion.
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Sub Querydocumentdelete(Source As Notesuidatabase, Continue As Variant)
Dim collection As NotesDocumentCollection
Dim note As NotesDocument
Dim recipents As String
Set collection = source.documents
recipents = "Deleted Entries"
While Not note Is Nothing
Call note.Send(False, recipents)