That could work also. It would definitely make it more useful.
Should the effect stack? I.e. refills empty quanta by 1 for each card on the stack
For example if you had 3 of these, any quanta pools that had under 3 quanta would get refilled to 3.
Very careful balancing would be needed if you want it to stack.
If you go for the cumulative effect, the quanta pool should only be refilled when emptied no matter how many ZPE you have played. (Refill to 3 if you have 3 ZPE and zero quantum in certain pool) This avoids a lot of abuse and makes it much easier to balance.
So would something like this work for wording?:
"If an element's quanta pool for either player drains to 0, it refills to N (3 times per turn per player). N = Stack size"
In other words, if your enemy plays a black hole, this would refill up to 3 of your quanta types to N. It would also do the same for your opponent, however, if you were to play a black hole on them.
It would make a much softer counter to quanta denial than sanctuary.
3 seemed like a good number there since it would put a single one of these on par with a quantum pillar in terms of output. It could be set to a different value though. I see some possible issues with fractal, but they would likely require getting a decent sized stack built up to be effective (stack size would need to match or exceed creature cost).