I had an issue a few years ago where the fuel pickup "sock" (strainer on the end of the pickup tube) inside the fuel tank was clogged and collapsing with the fuel pump trying to pull fuel from the tank. Letting it sit for an hour allowed the sock to relax and start letting fuel flow again, only to clog again a little while later. It was very frustrating.
My symptom was the fuel filter housing would empty of fuel, and I could not get it to prime at all until letting it sit for a while, so it may not be the same problem as yours.
I had to drop the fuel tank and swap out the sock on the pickup tube.
Casey
1995 K1500 Tahoe 2 door, 6.5LTD, 4L80E, NP241, 3.42's, 285/75R16 BFG K02's; 1997 506 block; Kennedy OPS harness, gauges, Quick Heat plugs, and TD-Max chip; Dtech FSD on FSD Cooler; vacuum pump deleted, HX35 turbo, Turbo Master, 3.5" Kennedy exhaust, F code intake; dual t/stats, HO water pump, Champion radiator; Racor fuel filter