This mod feels almost essential with the chemistry-focused mod Nullius, but it only seems to work partially — some buildings/recipes work normally, but some can only flip inputs or outputs. Any chance you could look into it?

Can you give an example?

Here's a simple save file demonstrating what I've encountered so far (haven't played all the way through). The Hydro plants and Distilleries seem to flip OK, the electrolyzers can't flip anything, and the chemical plants can only flip outputs. https://we.tl/t-VXLyHEe77y

Very peculiar. The recipes and fluid boxes get flipped (look into the machine to confirm the recipe changing), but the game does not change the outputs...

It is likely a mod loaded order issue.
I will look into it.

Any news on this problem?

i'm also having this problem

2 years later, still an issue.

I just fixed that on Fluid Permutation Fixed. :)