you sure GX just didn't get switched to emu-NAND mode or something? i am not as familiar with the inner workings of GX like i am with Wiifow, but it's gotta be something simple. if the games show on the computer, then they're there.
i do find it particularly puzzling (almost to the point of saying it's impossible) that GX would show 600GB free while the computer would only show 400gb free.....but like i said, i'm not as familiar with GX.
you could just delete/rename the config file for GX and let it rebuild it with everything default....or delete everything GX related and reinstall....
PS: your post sounds more like a rant than a plea for help....maybe punctuation wold help....just thought.