I don't work for Medicare so I cant say for sure if that is a red flag for future audits. However, we do voluntarily refund money back for charges billed in error. We also submit corrected claims to CMS after being paid on the original claims and they haven't audited the doctors because we submitted a corrected claim or red flagged the doctor in their system (at least not to my knowledge).
Normally, at least with First Coast Service Options (Florida's MAC) I have seen them process the corrected claim and offset the difference between the allowable from the first claim and the new claim. So for example, if we billed 69436/50 in error, was paid $274.21 and then submitted a corrected claim with just 69436, they've offset the difference (in this case the difference between $274.21 and $182.81 or $91.40). However, I cant say that I recall them ever offsetting our entire original claim just to pay the corrected claim. But I wouldn't rule it out. Normally when we have submitted corrected claims, we will receive an EOB showing the original claim being offset X amount and then we get the EOB for the corrected claim. Sometimes the EOBs are in the same remit, but usually they're in two different remits, a week or so apart.
Not all payers work like that though. Many payers want us to refund the money on the wrong codes first, submit the corrected claim, and then wait for the correct payment on the corrected claim. I don't necessarily like that process, because (more often than not) the provider has to be vigilant in following up on payment on the corrected claim; duplicate claim denials, bundling denials (bundling the new code to the old code we refunded), etc...don't get me started.
