There has been many forum posts similar like this. General rule is to have one PCB per project. Create secondary PCB project to contain the secondary PCB. Autorouter is most likely not programmed to understand that there is two PCBs on a same project. I sent you a PM if you are interested to accept my help on the project. Few things to note already, marked with orange:  Regards, Markus Virtanen HW / Electronics Designer