I could be wrong here, but I believe that during the initial configuration that since the rom path is altered from default that it knows to update the list. Given you just manually added and deleted some folders, this event wasn't triggered, so changing the roms path may prompt an update. Note that I have not tried this myself.
I don't recall a manual "update" in EVO like there is in the original GameEx, so if not it's a feature that needs to be added to address exactly the situation you're describing.
Out of curiosity, why did you delete the emulator?