When changing a tag question, for example:
It's only you who have that book, isn't it?
to a non-tag question:
Isn't it only you who have that book?
Does the verb stay the same?
No, the sentence is not grammatically correct. I'd word the question, "Aren't you the only one that has the book?" The subordinate clause, that has the book refers back to the singular pronoun, one, not you, so the singular verb, has, should be used.