Back when we were doing dairy, and switched from ultra-pasturized, lactose-free organic 2% milk to non-homogenized local lightly pasturized whole milk (and cream and butter), we noticed a complete change in our 'tolerance' for milk and milk products. Meaning, we COULD tolerate non-homogenzied milk products whereas our previous milk gave us (adults) pretty immediate intestinal problems (even lactose-free milk).
BUT I noticed that whenever we microwaved some of our new 'better' dairy-containing products, our intestinal problems returned. The high localized heat of the microwave (I think) was just blasting the heck out of the milk, causing the same digestive problems as 'homogenization' for us. This made me stop using the microwave for anything that I think of as being fatty or with protein in it. I do use it to heat up water and for very short bursts of time for various other things, but mostly we're not using the microwave anymore.