You have the right to be worried. I would return the intake ASAP.
The performance gain you are seeing right now is due to the MAF sensor being fooled into thinking there is less air than there actually is and the O2 sensors responding that the mix is too lean to self correct. The custom tune for the intake will basically cancel out the gains by bringing the fuel/air ratio back to what it should while also reducing cam timing and other things to silence the drone.
If you are dead set on keeping the intake, do not drive it or put the stock intake back on until you have the rewritten tunes.
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