Okay, I think i fixed it in v1.01 (in Downloads), now the swamp water prompt will only be visible if player party has An old cup (from basement) in the inventory and already read the recipe it's intended for, before this it showed a "Gather swamp water" dialogue box without yes/no option in a case you read the recipe but didn't take the Old cup. Thats how I understand the code I wrote a while back at least.
In any case, the correct order of actions is read the recipe -> loot the cup -> gather water -> ...
I have no ability to test if your savefile is fixable with this new version, but I hope it is, if not use latest version and click through the part of the game you already beaten (it won't take long).
Sorry for the inconvinience and hope this bug is finally fixed.
If you have time please give feedback if it was fixed for you and hoping to hear your thoughts and see your rating for the full game as it was intended to.