I think what your provider should do is "split bill" if he insists on using the V20.2. Bill out both the preventive and an E/M. The well child components will need to be separated from the "other issues", which will probably bring his E/M level down a notch or two. But, if you check the Vcode table in the ICD-9 - the V20.x codes are 1st Dx Only - with the memo of "generally for use as first listed only but may be used as additional if patient has more than one encounter on one day" .. NOT as 3rd or 4th dx on "one visit". MUST have MORE than one visit in one day if the V20.2 isn't going to be listed first - If the patient has only one visit, then the V20.2 is listed first - Sooooooooo: if he charges both a preventive (link the V20.2 to it) and an E/M with the other dx (and a modifier .25 on the E/M) that will work out. If your provider does decide to split bill, two separate notes would be a VERY good idea because each service must be supported by documentation and the documentation must be able to stand alone in support of each service! Note: patients (or in this case patients parents don't take kindly to "two charges" for one visit), your provider should be aware of that too.
all that being said - my personal opinion is - though the patient is special needs it's STILL their well child visit -I'd be upset as a parent if, just because my child had special needs that needed to be addressed a second charge was billed out OR that a higher cost E/M level is billed out (and I pay an office visit & copay), rather than the preventive service code when my insurance pays 100% for an annual well child visit, especially if the issues are chronic, nothing changing, just reviewing, etc...- after all, each persons annual physical is different, they don't treat us all the same. Most of us do have issues that need to be checked/updated/reviewed when we go in, but it IS still part of the annual physical review.
Check out the CSHCN in your area. (Children with Special Healthcare Needs Services Program).
{that's my opinion on the posted matter}