Yes, my doctor also gave me pancreatin (creon) alonside Antibiotics but it did not help me as in your case. Our case may be indigestion of food. As for the intestinal flora, they say that using probiotics is beneficial to alter that bad environment. However, I'm doubtful about its efficiency. Maybe I have to use another type of probiotics. I don't know. How long and in what dosage should it take for getting a perceivable effect?
To reduce ammonia level (if that is the case) it is suggested that lactulose may help. However relying on lactasives too much is not good for digestion. I was also not able to detect any change when I took lactulose in periods of constipation. The rotten smell is generally same to me no matter its form and quantity.