If you have a raised spa (higher than the pool) and you keep your valves in the positions shown your spa will drain. The handle on the return 3-way valve should point to the right completely (3 o'clock). The handle on the "drain" should also be in that position. The line labeled "spa waterfall" should be the line that returns some filtered water to the spa to keep it fresh. With the handles in the position in the pictures there is nothing from stopping a raised spa from draining back to the pool through the equipment. Your spa was drained today because water was being pulled from it through the open main drain valve but mostly returned to the pool.
Close the spa port on both valves and the problem should go away unless you do have a bad check valve. You would, usually, be able to see that through the lid of the check valve as water motion. I've seen this many times because pool owners/operators (new service techs) think that setting the valves as in your pictures will somehow improve circulation.