I would not ask a doctor. Doctors are not trained in pipe smoking. A doctor will just tell you to quit because they believe that all smoking always causes cancer. The only thing a doctor will do is offer you a pill that will cover up one symptom and cause various side effects. They have never been much help to me. Now I only go to doctors for broken bones, lacerations, and the like.
I think I know what you are talking about. If I let a half-smoked bowl sit for a little while, and then I come back to it, after I relight it the smoke it produces is much more spicy and somewhat sour and tangy. I enjoy it. My guess is that all the juices and nicotine from the partially burned tobacco marinate and intensify. The harsher smoke is more likely to irritate one's mouth or throat. Smoking causes me some oral discomfort and it can sometimes irritate my throat a bit. It's smoke.