Q: Why are my filtered out files and folders not deleted from the destination?
When a file or folder is filtered out, or unselected in the file & folder selection tree, you are explicitly telling SyncBack to ignore those files and folders. Because those files and folders are now being ignored (they are not part of the backup or sync) then SyncBack does not see them and therefore they are not deleted. You must manually delete those files & folders from the destination.
As an example of why having SyncBack delete filtered out files & folders from the destination is a bad idea, consider the following:
The source is X:\My Files\
The destination is C:\
You tell SyncBack to ignore the Windows folder
If you ran that profile, and SyncBack was configured to ignore the Windows folder, but you wanted it deleted because it is filtered out, then all your Windows operating system files would be deleted. Obviously this is not a desirable outcome.
A corollary of this is - for example - a scenario whereby you are backing up to a resource Destination that does its own unilateral indexing (or similar), creating folders and/or files for the purpose. If you are using a Mirror profile (and by definition, these objects generally do not exist on Source), the profile would ordinarily delete these Destination-only entries (along with files you do want deleted if (now?) absent from Source). But using filtering or de-selections, you can leverage the above behavior and prevent a profile doing so for the 'unilateral' entries, by telling it to Ignore them. (Again, it will do so on both sides, though Ignoring on Source is irrelevant in this example as they do not exist there anyway).
Another reason for not scanning unselected, or filtered, folders is performance. If SyncBack had to scan filtered or unselected folders (to know what to delete) then it would need to scan every folder and every file.