I say no, as long as you don't go into the deep code. If you are just changing the settings available to you, BMW doesn't care. I've changed all of my cars since the days before Bimmercode, when you had to use eSys, and all of those cars have ended up in for warranty service at some point and they never mentioned it to me.
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Current inventory:
F22 & G05
Cadillac CT5-V Blackwing w/3 pedals
Past: E24,E28(3),E34,E36,E37,E38(2),E39(4),E46,E89,E92 (obviously),F01,F06,F10,F30,F87,G12,G30(2),G82(2)
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