I'm interested in this scenario, too.
I add a remark. I have done a simulation with pc A (win8, sharing) and B(linux, receiving encrypted). When I delete a file from A (after it is sent to B, I've checked), it is NOT sent to archive. On B, the archive subfolder has not been created.
So, how can you state that "Simply cutting and pasting them back into the synced folder doesn't work as sync quickly sends them back to the archive folder."?
According to my result there is no deleted copy to cut and past with a single encrypted peer...