From SyncToy 2.0 - Frequently Asked Questions
Q. SyncToy 2.0 appears not to sync
deleted files when I have the sync
option set to 'Echo'
A. This can happen if the files are
updated on the right. This includes if
the file was touched by an anti-virus
program, music player, etc. To confirm
that this is indeed the case - change
the sync option to "Synchronize" and
do a "Preview" sync. Do NOT hit run
because this will sync changes from
the right to the left. If on a preview
you see updates from the right to the
left folder, this means it was changed
on the right. The only workaround in
this case would be to manually delete
the file on the right. And do not
forget to change your sync option back
I'm guessing this is your problem, because I just checked on my computer, the "Echo" deletes folders correctly.
Precisions on the "Echo". The "Echo" method in SyncToy will echo the changes from left to right. But to avoid losing data, it won't take care about folders and files created after. Typically, in your case, you want it to delete the folders you created after, but in general, I doubt you expect the backup tool to erase data it's not supposed to take care of.