Most physicians are not very knowledgeable about coding. He may not even be aware that a combination code exists. (Or may not care to document it separately.)
With documentation stating polyneuropathy due to diabetes, that would certainly be E11.42 (or E10.42 if the documentation showed T1D).
At my employer, I would make the change on the claim myself without consulting the physician. I code based on what's supported in the documentation and have the freedom to do so without running it by my physicians every time.
However, I know that not every office is like that. In some offices, coders feel like they can't change the numeric code the physician selected from the list, even if the language used in the documentation actually supports a different code. (I don't necessarily understand why a practice wouldn't allow a certified coder to utilize their expertise to ensure the correct code is being billed, but some offices are like that.)
I'd talk with your physician and clarify how he'd prefer you to handle this and similar future situations.
Would he rather you run it by him every time? Or would he rather you update to the correct code when the documentation states something as clear cut as "polyneuropathy due to diabetes"?