Yep...this used to be the case when using Dinan flash-tuning; fortunately for me, the dealership did the Dinan flashing as well, so whenever there was a software update applied (such as during the infamous HPFP issues with N54 engines), they'd always re-flash my previous E92. Cobb's tuner, on the other hand, would not do a complete reflash, but only certain mapping paramenters. Whenever a new BMW software flash was applied, the Cobb unit could then add back their updates. Custom (FDL) coding always had to be re-done afterwards in either case.
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2015 F80 ///M3 Sedan 7DCT Tanzanite, 2022 X3 sDrive30i 8AT Brooklyn Grey
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