Maybe you can use separate battery sensors for telemetry instead of the integrated one. https://meshtastic.org/docs/configuration/module/telemetry/

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Yeah, good point. I have an ammeter circuit and it shoul be able to be used to measure a secondary battery.

Depending on how it is connected, it could impede with powering the device (as I found out the hard way). But if it's independent of the primary battery charge/discharge, it should work.