Some of the tuners will recalibrate their chips at least once free of charge, while others charge each and every time. As a matter of fact, one of the popular tuners charges extra to begin with if they take their existing chip off of the shelf and recalibrate it if you have headers. Their standard chip reduces fueling by half of the stock setting, but with headers they recommend you have the 6% rich fuel delivery, so they charge extra on top of their price to do it.
The question is did you take that into consideration when buying a chip from them?
Have you needed to have your chip recalibrated for any reason?