Of course it will affect the warranty. A 50mm lift causes the glovebox to be at a higher altitude so the latching mechanism won't be as effective in the thinner air. Expect everything inside to fly out at random intervals as the raised paint on the road slams your rear suspension against the bump stop.
Seriously - the dealer MIGHT try pulling stunts. Nissan might too. But unless your problem is in some way caused by the change, they have NO right to refuse warranty.