When you are plugged in to shore power, the BIRD should sense the charge status of house batteries and the chassis battery. The BIRD should provide signals to the Isolation Relay to allow the relay to connect and disconnect the charging circuit of the converter keeping your house and chassis batteries charged. You said your house batteries are charged but the chassis battery is dead.
Here is a link to my manual:
https://1drv.ms/w/s!AiYx6DLSeiiP53x246awlGrg8B-I
Go to Appendix 4 and read the description of how the BIRD, Trombetta, and disconnect relays work together on pages 112 and 113. Look at the diagram on page 115. That is how they are connected. On that diagram is a switch labeled "Aux Start on Dash." This is the Emergency Start switch on your dash under the radio. When you push that switch it should jump the house batteries to the chassis battery through the Trombetta Isolation Relay and allow you to start the engine using the house batteries jumped to the chassis battery. Depress and hold the Emergency Start switch, and while depressing the switch turn the key in the ignition to try to start the engine.
Folks already discussed the manual battery disconnect relay next to the batteries. Be sure you have engaged that relay -- yellow flag NOT SHOWING, and red button sticking out.
If you chassis battery was not charging while plugged in to shore power you probably have a bad BIRD, bad Trombetta, or Thor did not wire the Trombetta and disconnects correctly. Several owners have found those components bad, or improperly wired. Ron & Kay even found that their dealer had cannibalized the house disconnect relay had had not told anyone about it.
And be sure the STORE/USE switch is in USE. House batteries WILL NOT charge if the switch is in Store. The Store position electrically disconnects the house batteries from the RV.