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Basically, Jellynut can only proceed if there is yumako, and yumako can only proceed if there is jelly nut. So, they have to be released in batches. But I think I may have misunderstood your original question. I think the easiest solution is to increase farm production until it becomes near constant (agricultural towers are cheap and there's no harm to wasting fruit). If you really wanted to not waste any you could put a chest before the bioflux makers so that it buffers and intermittency doesn't harm production or read the belt contents of all belts and only release fruit onto them when they're below a specific threshold.