So my seeds and plants exist in the world and in my RS system along with the essences, I can no longer craft the expected output (or anything else) with the essences and the seeds won't go through the seed repressor an longer.
I would think if they were completely removed from the modpack the farm would have empty plots of land and all of the above would have vanished from my RS system, so perhaps it is a recipe(s) missing?

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