There MAY be some more qualified opinions on here since a couple guys specifically worked as finishers but my experience and understanding says you should be fine.
What usually causes chemical issues to arise comes less from the finish itself and more with thinner that's mixed into it to make it a liquid and/or to make it sprayable. The paint is essentially loaded with an alcohol-like thinner that evaporates and leaves behind the actual medium (color or clear). USUALLY the chemical mismatch is because the specific thinner in one paint doesn't like the medium or the thinner in the other.
The nitro is that type of finish (thins with normal lacquer thinner) but the urethane is a catalyzed finish, where it's mixed in two parts and they react to eachother to form a solid. Urethane stabilizes near completely when it solidifies. Assuming your nitro is totally hardened, they shouldn't really mix at all. I don't think the combination of finishes you're using is uncommon either.