What kind of mods are you talking about? If you are talking about exhaust or intake and the likes you should be OK. You can do a few things, disconnect your battery cables for a few hours and reconnect, or do nothing. The ECU should reset itself. I got a few warning codes thrown at me for like a week *check engine light was on* but it went away, I figure it was the ecu adjusting to the better breathing. Hope that helps.