I guess you mean the option to "look for enabled duplicates"? If so, it's in Font Book > Menu Bar > Edit (⌘L). Well, at least that's where I noted it.
Found it. Ran it. No enabled duplicates. 'Tis a poser. But as I said, no functionality issues associated with the phenomenon; it's just weird and whatever it is merely utilizes processor resources for no apparent reason. Ah well ....
