Good morning! This had been bugging me. With the MPV in closed, your IN & OUT ports should be closed. The only exception might be WASTE which I believe would still be open and why you noticed water could indeed overflow out thru that waste line during the deep clean. That's also how you recovered that air relief vent screen. With a side mount, you don't have a tall center pipe that goes from the bottom (laterals) straight up to the very top of the filter collar like a top mount MPV. Instead you have that diffuser that was attached to the top inlet elbow pipe. That's what we could see exposed about 1/4 down in your pic. It's good you placed the coffee filter over it. Always best to cover that pipe. Some people also close any 3-way valves on the equipment pad before and after the filter as a precaution, but I don't understand how anything could've gotten past that MPV into the pool while in the closed position.

If I did up more info on that I'll let you know for future reference.
In any case, it's good you inspected and fluffed-up the sand to get things moving again. Hopefully you begin to see more improvement today. If not, we'll regroup and see what your next best option should be.