Not a worry mate.
In my opinion, the value stays the same if not increases it as it's a far better car to drive, now it is a manual. Best to always get it checked by a professional that the conversion was done correctly if you can't spot stuff like, dodgy wiring, hacked firewall for the clutch master cyl etc, yourself.
The auto's aren't a bad thing, they're very reliable, but they're not great for nearly all things that involve spirited driving. ?