Dont worry - did a very similar speaker /amp upgrade path on my G30 with base audio - simply a case of coding (aka changing a parameter) to output the flat hi-fi signal instead of the basic audio eq'd noise. Just changed within the NBT2 settings, you'll know when you see it.
Sounds fantastic now, especially with the less harsh Eton tweeter (ive had factory HK in previous 3ers and 5ers).
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