Well it's most likely not a suction line, so digging up your deck probably isn't in your future. Air being entered into the system via a suction line would occur during filtering. Yours clears up right away. If there was a problem with a suction line, you'd get intermittent bubbles in your pump, then out the returns.
Sounds to me, somehow some air got into your filter, piping, pump or all three via the "topside". The water wants to drain down back into the pool, unless your entire system is below the level of the water in the pool. Think of liquid in a straw with your finger on top of it. Once there's even a tiny leak of air the water "drops", leaving air in its place.
You might have a gasket somewhere that's getting a little old or dray and is not quite sealed. It might not show as a leak as the pump runs but only as air in the system when it sits for long periods of time.
When a system loses "prime" during periods of idleness, but yet doesn't show any "drips". It's a sign that the "leak" allowing the water to drain lower and leave a pocket of air is on the suction side. Since when the pool is running it's not forcing the water "out" the same leak. Pump lid? Winterization plugs? If it's forward of the point of suction (front of pump where lines go in) , it would most likely pull air, in the form of intermittent bubbles.
I'd "batten" down all the hatches by tighten things. Tighten them by hand and don't force them, most pool equipment is meant to be "hand tightened". Once they seem tight by hand that's really as far as you should go. If you feel you don't have adequate strength you can use a tool of some type (Chanel Locks or pliers), but do it very gingerly and with care.
So go through every thing "topside". The pump lid (window) thumbscrews, even check the winterization "plugs" in the body of the pump. The bleeder on the top of the filter, and even the two unions connecting the multi-port, don't forget the drain plug too (but that would show moisture) . Any "union" or other fitting not glued can be addressed by just checking to see if it's tight or not, any of them could be a suspect. Give em all a good "twist" you might find one that has loosened because of the "jerking" of the pump when it goes on and off, or because a gasket has become older, drier , and thus smaller.
Even something as simple as not seating the multi-port selector just right can cause air to infiltrate from the backwash line. Did you backwash and re-earth the filter previously to this problem? Perhaps the very night before? Did you dissemble the filter and clean the "grids" recently? Perhaps the seal between the two filter body halves isn't perfect.
I wouldn't be too concerned, even if it is a "leak" it's most likely topside by the very fact the system re-primes itself on its own. It's most likely something that can be addressed with a "part" or gasket.
The difficulty with trouble shooting this type of problem is: the problem doesn't last long. By the time you go to do anything or reproduce it, it's gone. Not a bad "problem" to have, one that goes away.
Good Luck.
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