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Ever heard of diapers? I have also seen people with a bag connected to their intestine. With a sufficiently large bag, I don't think gastrointestinal problems like the one you mentioned would be an insurmountable obstacle.
The last thing you would want is to throw up in the patient's open stomach.
That reminds me of the Seinfeld episode when Kramer and Jerry were watching a surgery from above the surgery room. Kramer was eating junior mints, and he accidentally dropped one and it fell inside the patient's stomach. The doctors didn't see and sutured the patient back up with the junior mint inside.