So, I saw some youtubers using a Ender IO farming station to automate Magical Crops. So, I thought,"hey, I'll try and use that to get my resources more efficiently. So I grinded, exhausted most if my resources, and got my farming station, as soon as I gave it what it needed, instead of it harvesting the crops like it would've if I'd used my fist, it harvested the essence and the crop was gone. I was lucky enough to have some back-up seeds so I wasn't entirely ruined, but I want to know how to fix this so I can get back on my feet, and move on.
Go into Magical Crop's mod options, and set the option for crops to replant themselves when harvested to true. The Farming Station should work normally after that change.