I think i found out why only some shortcuts went missing. Some installers create a shortcut on desktop, or in Start menu, so that ones didnt get deleted. But the ones that just create a shortcut in Game Explorer, and i made a copy on desktop from the Games Explorer, they are considered invalid, even though if you click them and the open the game normally. The maintenance tools thinks they are invalid, because they point to Games Explorer.
Kind of stupid, since they work perfect, but at least i found why only half were gone.
Thanks for the help everyone!