Hello!
I'm not sure if this was a recent update which broke this (as I know valves were added into the game itself, etc), or if I just hadn't set up this exact thing and noticed its incorrect behavior before.
[pipe system A]->Overflow valve->pump->[pipe system B] is broken.
Expected behavior: When A is over "X% full", we'll go with 50% for this example, then it would overflow into the pump, which would then "pressurize" pipe system B. Such that after enough resources have overflown, system B would eventually get 100% full. I used this system all the time in Factorio 1.1 and modded runs and such.
Actual behavior: the pump pulls out of the overflow valve REGARDLESS of its "fullness". Yep. It just 100% empties system A. Even though there's an overflow valve that should be stopping flow when system A isn't actually full enough.
I'm not sure if this is even fixable or is some weird result of the new ways that valves work and such, but I would consider it a fairly critical bug and hopefully some sort of fix can be found, as it's base-breaking level issues.
If a fix cannot be found/made, I would actually recommend adding a check for the overflow valve->pump placement combination and giving a warning to the player. As there's no reason they would assume that it would fail.
I'm not sure if top-ups have any issues, but I think they're fine. Guess it would be worth testing if pump->top up->system B doesn't overfill system B?