Of course you lose primes when you empty the tanks
Any time the level in the tank drops below the top of the discharge fitting, the pump is gonna start sucking air and lose prime. Fill the tank high enough to completely cover the discharge fitting, and the pump primes again.However, I wasn't aware that these boats have two linked tanks. Without seeing what's happening, all I can do is take a guess that when the boat is heeled, ALL the water is running back into one tank, causing the pump to suck air from the other one. That WOULD prevent it from priming until the two tanks have equalized again--or at least until both discharge fittings in both tanks are completely below the water level again. Or...if the water level is low enough and the empty tank is lower in the boat than the one that ends up with all the water in it due to heeling, they may never be able to equalize enough to allow the pump to prime again till more water is addded...or, if the diameter of the manifold is small, it may just take so long to equalize that you give up. Whatever IS happening, it's happening because something is causing the pump to either pull a vacuum or suck air after the boat has been on whichever tack for long enough to make it happen...'cuz water pumps don't get "air locks"--they only refuse to prime if water isn't getting to 'em or they're pulling against a vacuum. Figure out how to prevent whichever it is, and you solve the problem.