Did you try another FTP Program not Multiman ? eg. an old Black box FTP may help to find the games. There are also a lot more radical solutions like wiping the HDD via recovery menu. Have you tried to rebuild the file system ?
And you always can format the HDD via PC and then restore factory settings on the PS3, re install MM and you should be fine. But pls backup you saves and PSN/DLC content first (don forget the raf's and act's) MM names the game folders normally with their BLUS or so and their name, MM uses a redirection and part of Sonys tools so if not named correctly the content can't be seen by the PS3 , the machine is picky in this way. It sounds to that you dammed the PS3's "registry" or the listing of MM.
If you can find the files via Black Box FTP delete them restore file system and recopy them with MM but I fear you have to take a more drastic route like I mentioned.