Let's say, John owns two death notes. One belongs to Ryuk and the other belongs to for Example Ragnarok. He makes the eyedeal with Ryuk, then, he gives ownership from the death note Ragnarok brought him. Will he now lose the shingiami eyes?
On chapter 5, Ryuk stated that the shinigami eye was a deal between the shinigami and the human owner of a certain note, so it will probably be associated to that relationship, so the eye will be gone as soon as the shinigami leaves his side.