I think you can get an O2 sensor which fakes the reading. The warning light won't go away because your O2 sensor is not reading what it should due to your high flow cat/s. So you'll need to change something either the sensor or the tune to make the car happy. I also would have thought if you had APR do a tune they could probably disable/change the warning in tune, have you spoken to them about it?
As a side note, did you notice a difference with the tune? Is this a 3.6L?
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