Over on
this thread there's instructions on how to push a mod onto an existing savegame. I used those steps to make a couple proof of concept recipes in ItemCombos / ItemComboPreviews and they worked in my current save.
Then I went ahead and "fixed" the Joshua Spice recipes based on the bug you pointed out. That did the trick!

(I went ahead and made a recipe of carrot + pear to produce the spice, so I could test it with what I had on hand.)
So, technically we could fix them - or, well, add a whole bunch of new recipes for stuff that's "missing" - right now without waiting for Larian. But maybe that needs a different thread of its own...
