The battery seperator is a relay which closes (connects) when the house batteries see 13.2volts linking the chassis battery to the house batteries so they are both charged, and opens (disconnects) when the batteries hit 12.6-.7 volts when the ignition is off (12.2 volts when on) preventing the chassis battery from being discharged.
Unless something is wrong with the seperator, the house cannot discharge the coach battery much. It sounds like you have a bad chassis battery.
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