Audit for 99211 billing

I'm a physician who learned coding and billing from the ICD-9 and CPT® books, not per the insurance company conventions which seem to be widely taught.
Our practice has been audited and the insurer is asking for money back. There are 2 issues:
1. We've used 99211 for single immunizations. We've been paid, for several years. It does meet all the criteria for a level 99211. However the CPT® book does specify the 90471-3 or 90460/90461 series of codes, thus trumping the conceptual use of 99211 for this purpose. Although it is arguably defensible to use the concept of a 99211 applied to an immunization, the consensus in the billing community agrees with their interpretation. So I agreed to negotiate a settlement of this issue for the prior 18 months, the maximum allowed take-back period for our state of NJ. The exceptions to this time-limit are for fraud or abuse which are not issues. The insurer wants to negotiate from 6 years back.
2. We have billed 99211 for such things as issuing referrals required by this insurer and for such things as medication refills, lab orders and other administrative purposes as per Appendix C in CPT®. Of course the patient is required to present in office; these are not for phone encounters. We have used ICD-9 codes, V68.81, V68.1 and V68.09 for such things. These are valid codes used in the sense of the Clinical Examples in Appendix C, the heading of which calls it an integral part of the coding/billing process. This insurer states that these are invalid codes but yet have paid for 6 years and now want to take back payment. They also argue, in case they can't prevail on that score, that the level of service is not sufficient. However, in reviewing the CPT® book in this regard, no requirements are given for this level of service for History, Exam or Medical Decision Making. Since all other office visits require at least some of these, it follows that a description of the service provided is sufficient documentation. On this issue I did not agree to negotiate and will vigorously defend our past billing, though going forward we may have to negotiate an agreement.

Does anyone have any wisdom to share on these issues? I know this is unconventional. That's why we were audited, as an outlier. But convention is not enforceable and if the AMA source books support it, then why should we yield to the opinion of the insurer? I should note that this insurer is a Medicaid HMO that has a flat rate of $40 for all 99211 to 99215 office visits, meaning that a 99211 is paid the same as a 99215, quite unconventional. Their rep says it evens out in the end, though it seems they didn't like how this worked for us.

re: Audit for 99211 billing

Do you have a contract with this Medicaid HMO plan? If so, most contracts allow a certain time to go back and collect overpayments. I would review that first. Also, I am not sure what state you are from but there is no CPT® 90471 in the Medicaid Fee Schedule in Florida. At least none that I found, so CPT® 99211 would be appropiate. If you have no contract with them and there is no CPT® 90471, etc.. in the fee schedule then they have no basis for their claim. Definitely check the laws in your state.