A 2-position valve on a sand filter is not a good installation. You should have a multi-port valve installed. With the valve you have, whether using sand or a Zeo product you will always have some of the filter media return to the pool until the filter bed is compacted. That is why there is a rinse postion on the multi-port valves.
Any time you open your system you allow air in. This will allow the water to drain. It should not be enough to cause your pump not to prime. Just put the lid back on and start the pump. Make sure that the lid "O" ring is lightly lubricated at all times.
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