The setting you mention (on the Fast Backup settings page) is nothing to do with deleting 'orphans' on Destination that no longer exist on Source. It's to delete (flush) all files from the 'differential folders' it is pointing at on the run in question, so that (in a weekly cycle, purely as a simple example) today's backup is not 'polluted' with last Thursday's changed files (which have presumably been backed up in a Full (Rescan) backup at some point since last Thursday anyway).
Notice how it says 'all' the files on Destination, but also says '(only if not a rescan'). You wouldn't want to delete all files from Dest first in a Rescan, then re-copy everything that still exists on Source (very inefficient...) - so we don't. If it's a Rescan, it ignores that setting - as per the Help
...The files and folders are not deleted if a re-scan has been forced or is required.
We did actually go over the above in another thread of yours a couple of months ago.
If you want to delete orphans, use the settings on Decisions-Files to do so (that is, change the profile to a Mirror). Or, providing you run it manually so that the Differences window appears, you can keep it as a Backup, but 'on demand' use the override button on the Differences window to
'Mirror all the files/folders to Destination'
which will do that as a one-off-only operation (next run will default back to Backup again). Make sure you pick the correct override (the other one will may potentially delete stuff on Source that is not on Dest, etc). Using the overrides will change the proposed actions in the grid above. It is up to you to review the new proposed Actions and make sure the actions are what you want.
Notice how it says 'all' the files on Destination, but also says '(only if not a rescan'). You wouldn't want to delete all files from Dest first in a Rescan, then re-copy everything that still exists on Source (very inefficient...) - so we don't. If it's a Rescan, it ignores that setting - as per the Help
...The files and folders are not deleted if a re-scan has been forced or is required.
We did actually go over the above in another thread of yours a couple of months ago.
If you want to delete orphans, use the settings on Decisions-Files to do so (that is, change the profile to a Mirror). Or, providing you run it manually so that the Differences window appears, you can keep it as a Backup, but 'on demand' use the override button on the Differences window to
'Mirror all the files/folders to Destination'
which will do that as a one-off-only operation (next run will default back to Backup again). Make sure you pick the correct override (the other one will may potentially delete stuff on Source that is not on Dest, etc). Using the overrides will change the proposed actions in the grid above. It is up to you to review the new proposed Actions and make sure the actions are what you want.