When calling replaceInput on a recipe that has multiple tags per input item, the replacement is not done per tag. This causes the recipe to be potentially restricted more than may be intended.

Example recipe
https://github.com/CoFH/ThermalExpansion/blob/main/src/main/resources/data/thermal/recipes/machine/smelter/smelter_alloy_invar.json

KubeJS 1605-3-14 build 67.

Do you have an example script with expected inputs and outputs?

Taking a shot in the dark from the way you described it, and using the provided json recipe, if you replaceInput for forge:ingots/iron, it doesn't just replace forge:ingots/iron, it fully replaces that ingredient (both forge:ingots/iron and forge:dusts/iron) correct?