After IBD symptoms have abated for several months, many beans and lentils are "legal" on the specific carbohydrate diet.  To make the beans more digestible, the usual procedure is to let them soak overnight before cooking.  The Mayo Clinic's website also has instructions for a "gas-free soak".  The instructions appear below:

Gas-free soak. In a stockpot, place 1 pound of beans in 10 or more cups of boiling water. Boil for 2 to 3 minutes. Then cover and set aside overnight. The next day 75 to 90 percent of the indigestible sugars that cause gas will have dissolved into the soaking water.  [Note: rinse the beans after soaking]

source: http://www.mayoclinic.com/health/legumes/nu00260

Note: Some legumes are not allowed on the SCD: chick peas, bean sprouts, soybeans, mungbeans, faba beans, and garbanzo beans. 

Allowed legumes include: Dried navy beans, lentils, peas, split peas, adzuki beans, and lima beans. 

If you have a question about a specific legume, please search for it on the legal/illegal list, this UCLBS posting, or ask us.