I read the entire font book help and the info in one of my books and it said deleting the font was "permanent" - I guess it meant from font book and not the hdd.
Dragging a font out of Font book didn't work for me, but I right-click removed and that worked. I deleted the library I'd added from font book w/out deleting the folder on the hdd.
After I deleted the library I checked my collections to see if the removed fonts were also removed from them and noticed some disabled fonts. So those fonts stayed disabled on reboot. Do you think too many fonts being installed could have prevented disable from working? Are disabled fonts supposed to stay disabled on reboot?