If the batteries are connected in parallel --> both batteries will have the same voltage.
And if your idea is to temporarily disconnect both batteries to do the measurement, then I don't think you will gain some information from the two measurements.
What's the idea behind this setup?
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Now you say "hot swap".
Then I recommend to use a mosfet for each battery...controlled by the microcontroller.
Or at least an "ideal diode" device not to waste too much energy.