You can simply disconnect them, but depending on your factory amp (assume you are still using it, right?), it may be sending some frequencies to the midranges that are not being sent to the other speakers. If that is the case, you will lose some important sound--especially vocals.

Your best bet is to replace the mids with something of equal quality to the components you put in the doors. BSW sells 2.5-inch pairs for just this purpose, or if you don't mind a little wiring work yourself, just get your own 2.5's and wire them in.

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85 M635, 89 Z1, 90 Z1, 91 850, 02 4.6is, 03 M3 Cabrio, 17 30-Jahre M3