Enteral nutrition usually is designed to avoid food intolerances/allergies. It accomplishes that by using amino acids instead of proteins. The immune reaction causing allergic reactions is a response to proteins. They may still cause trouble in other ways. The problems, if any relate to the carbohydrate/sugar components. If they are not digested nearly completely, it can end up causing bacterial growth in the gut. One of the difficulties that they have in treating this disease is that it can be an intolerance to food or to intestinal bacteria or their products or both. Further, there is an autoimmune component - the immune response to gut contents also cross-reacts to body tissue. The problem is to eliminate or greatly reduce the food allergens and bacterial triggers. Both of these can be done with diet.
You already know about
the use of enteral nutrition to induce a remission. You should then use the guidelines from the SCD (Specific Carbohydrate Diet) to introduce foods into his diet. In fact the SCD uses a simplified version of enteral nutrition as its starting point. For more information, see:
http://www.scdiet.org/ or
http://pecanbread.com/p/how/protocol.html and the information under "stages".