There are no errors related to this issue. However, a Dtrace of the EVLotusDominoJournal task can verify that the issue is occurring due to the journal task.
If the Journal task is deleting the items from the source, a line similar to the one below will appear in the dtrace log for each item being deleted:
28014 13:11:05.496 [9128] (EvLotusDominoJournalTask) <11984> EV-M {DominoItemProcessor.PostProcessItem} Deleted note NoteId-4ddfe from DOM01/EVDOM!!journal\mailjrn.nsf
This behavior is as designed. The 'Safety Copies' tab on the vault store properties determines if safety copies will be kept and where they will be stored if 'Remove Original Items' is selected. The check box does not determine if the original will be deleted after archiving. The original item will be deleted whether or not 'Remove Original Items' is selected.
This behavior is as designed. Use as is.
When 'Remove Original Items' is deselected, the original item will be deleted immediately after it is archived.
When 'Remove Original Items' is selected, the original item will be deleted according to the 'Default Behavior' setting after the item has successfully been backed up or replicated on the partition.