I asked Mike at N54Tuning about this possible issue. Here is his response:
Originally Posted by Mike@N54Tuning.com
The Stage1 has MAF control so it doesn't trigger the tuner code, but if you are really worried you can also get the BT cable or CT to delete hidden codes.
328i M-Sport, Estoril Blue, Carbon XP 35 Tint, front heated seats, black Dakota, Sports Suspension, Anthracite Headliner, HUD, Pro Nav, Sunroof, hk 600w, Bi-Xenon, 19" 403M wheels, Reversing Camera, DAB+, Xenon, BT Ext Connect. JB4 on Map 2 with Catless DP produces awesome performance in Sport.