Great question! Let's use the example of someone who has had their gallbladder removed.
Even when the gallbladder is removed, the energetics of it remain. The Gallbladder meridian is still there, so a person can still have symptoms associated with Qi stagnation along the pathway (like sciatic pain).
The organs are viewed very differently from the Chinese medical perspective. When I refer to "Gallbladder" in this case, it includes the physical organ as well as the meridian and points.
Therefore, working the organ meridian will still have effects and benefits even after the organ has been removed.