Don't know about this specific case, but in the lite-novels, the familiars seem to exist as seperate entities, (unlike in the anime,) merging with their witches when they don their stikers/use their magic.
So I would guess that when they are not joined, someone with ill-intent could harm a familiar. (Or the familar could be killed in some kind of accident.)
Again, I have no idea about the specific case. Maybe the Neuroi did something?