Good luck with your new venture, i like to run bleach through my nft system once in a while to try and sterilise it. I do it when the lights are out and leave it in for about an hour before flushing it out and starting again.
Done it in coco but that was run to waste, not sure how well that would work for autopots but doesnt that system have a drainage pipe?
So long as you can drain and flush id go with bleach, works well with no noticeable side effects and saves buying another product