Actually Thog, FlashFXP has added this exact option based off a similar request to yours.
If you goto the menu Tools > Compare Folders, or press CTRL+D, you will see FlashFXP select all of the files that do not exist on each side. This allows you to delete the selected files on the Local pane, and queue/download the selected files on the Remote pane.
Vuala! A perfect mirror.
Enjoy.