Ive been experiencing this problem: after installing fonts using fontbook (yes I know....) it copied fonts from their original location to the system folder's fonts. No problems until I decide to delete sets in fontbook. After that, fonts werent restrored to their original folders (where they are all sorted in categories and foundries). Mainly, they just disappeared.

I've read something about font cache. there's a file called fonttablesannex that stores information about active and innactive fonts. this file weights 90mb. I think my fonts are still in there but I dont know how to get them back.

I think thats all the information I can supply right now.

thank you for your time