I had to actively push myself out of thinking this way. When a game hands something like a consumable to the player, it should be expected that they could use it at any point in time. If that item is non-renewable and certain encounters are designed around needing that item, then you actually playing a puzzle game that lets you permanently destroy the puzzle pieces with no warning.

Crystal Project does exactly that. The DoT effects do health percent damage, and the stronger enemies and bosses have resistance to it rather than full on immunity.