After more investigation, with big help from l3mce (thanks again), i can safely draw the conclusion that it was me who has screwed things up. What probably happened is that i ripped my cd's to the OS-Drive instead of the media drive.
LMCE doesn't delete files
I swapped my old OS-drive for a new one, so thats why they are not there anymore
Thanks for al your replies and help.
Look on the bright side: hopefully someone can learn from this, especially from the kick-ass commands from l3mce.