Although this is an old question, I’m adding some info in here in the case that somebody stumbles into this.
The bottom microphone in almost all iPhones is part of the charge port connector assembly. The microphone(s) live on arm of this cable. Damage to that cable in general is not uncommon, but more than likely something in the charge port assembly got nicked during battery removal. The mic on top is the primary mic and is labeled a “Mic1” by the system. The other microphone is probably for noise isolation or filtration.
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