There is an app manifest in the folder. So when it does an install it creates an .itch file with a small, what looks like, xml document that tracks what the app is. It's basically exactly what Steam does when it does an install. The trick would be to be able to have the app itself search and locate them or be able to manually direct it to an item the way GOG galaxy does by having you choose the game and then point to the install if the launcher can't figure it out.
Hopefully an itch.io dev will see this and have some info or a solution. :)