gas deletion

I downloaded the save file to see what's going on.

There's a bit of salt next to the salt water geyser. Clearly, the pump caused tiny amounts of salt water to vaporize, but there's neither condensed water nor steam in the room. The pump must have sucked up the condensed water and tried to move it to the infinite storage room, which, of course, would cause both hydrogen and water to be deleted since there isn't room for a 3rd fluid.

The above comment seems to be correct. The gas gets deleted because a second liquid makes it to the liquid vent. You can see the hydrogen slowly getting deleted every time a small packet of water makes it to the storage.

You usually put a sensor next to pumps in closed up geysers to not let it be a vacuum (for gas vents) or not draw partial small packets (for liquid geysers). Or at least have a gas to equalize the temperatures around liquid geysers. Pump working in vacuum is never a good idea