Even if we don't know exactly where Pluto is, we do know enough about orbital mechanics to have a very good idea of where it will be. Plus, they would run simulations of the solar system to take into account the fluctuations due to gravitational forces of the other planets.

Neptune has only completed one complete orbit since discovery. It was discovered in September 1846 and has an orbital period of 164.8 years. So, it would have completed an orbit in 2011.