By flavor chemicals, he may simply mean any chemical that has a “flavor”, whether that just be what is in the whey, olive oil, or oats (although he did add some ethyl vanillin, possibly other things. Same would apply). Flavor is mostly perceived in the nose, and the quality that makes something have a flavor generally has to do with it having a low vapor pressure and being easily released into the air. This means that over time, whatever flavor any food would have will dissipate.
The nutrients themselves aren’t breaking down, but whatever is flavoring a food is usually some other chemical present in small amounts. The same is true for food. It always tastes better when it is fresh, but it generally doesn’t lose a lot of nutrition from aging.