The duckbill check valve in the water fill cap is used / needed whenever you are not using the Tower Cap (which has a built in duckbill).  For example, when using the AquaCure Torch.
The vacuum that forms, as hot gasses cool, and sucks the water back into the electrolyzer (from the humidifier or bubblers) is normal, all electrolyzers form a vacuum when their hot gasses cool.
Backfilling causes the electrolyzer to over-fill, so that the next time gas is produced, lye solution is ejected out with the gas.
Most electrolyzers solve this backfilling issue by adding a check valve to only allow gas/liquid to flow OUT of the electrolyzer but not IN.
But check valves can (and often do) FAIL (for many reasons) allowing the backfilling anyway.