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It could have been located away from view on the other side of the motherboard, as is sometimes the case.

As for what the full intended purpose and potential capabilities of these secondary batteries are, I have no idea since that's not documented. I do know that it's for a whole lot more than an RTC, however.

Actually, regardless of whether or not smartphones have a removable battery, there's always a small second battery connected to the baseband for emergency purposes. I've confirmed this firsthand by taking apart several models, and you make out small coin cells on most online disassembly documentation as well.

The one in my old Atrix was a good 250mAh.