Hemp milk on SCD diet

My son is 2 1/2 years old and has been diagnosed with autism. He is allergic to milk, soy, yogurt, nuts, rice, corn and many other items. He loves his hemp milk (without suger) in a bottle before bed. Do we have to break him off the bottle before trying the diet??? I really hate to do this as he finds great comfort in having his bottle before bed. He has had a terrible time digesting food lately-- there are huge chunks of undigested food in his stool and I feel we have to do something very soon!!! Thank you! Any advice would be appreciated~~~~