Atum 2 has built in mod support! You don't need any other mods for this to work!

Quern

Adding a Recipe

<recipetype:atum:quern>.addRecipe(input, output, rotations);

Adds a recipe with the specified input & output, that takes the specified rotations to complete querning

ZenScript
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<recipetype:atum:quern>.addRecipe(<item:atum:fertile_soil>, <item:atum:fertile_soil_pile>, 3);

Removing a Recipe

Remove Recipes by Output

<recipetype:atum:quern>.removeRecipeByOutput(output);

Removes all recipes where the output result is the provided IItemStack.

ZenScript
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<recipetype:atum:quern>.removeRecipeByOutput(<item:atum:emmer_flour>);

Remove Recipes by Output & Input

<recipetype:atum:quern>.removeRecipeByOutputInput(output, input);

Removes the specific recipe, with the specified output & input

ZenScript
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<recipetype:atum:quern>.removeRecipeByOutputInput(<item:atum:emmer_flour>, <item:atum:emmer>);

Other removal methods

See Recipe Managers for other ways to remove Quern recipes