If the skimmers do not loose their prime it is unlikely to be related to the (but still worth checking)
a) pump basket lid & gasket
b) the pump suction inlet.

Have you ever had enough debris in the bottom of the pool to clog the mesh grill on the main drain? I once had a plastic pipe collapse at a glued fitting when by mistake a valve was closed on the suction side.

I would start by removing the suction manifold at the valves and pump and making sure all the "O" rings are in good order on the valve stem and the valve body to manifold joint, if they are then I would be looking at making up a fitting to back flush the main drain line, just in case there is a blockage and before you start digging things up.
Best of Luck!