A1: By default, CYPD3125 have pre-programmed I2C bootloader. For your case:
a. If you only boot-loading CYPD3125-40LQXI_notebook_one_3_1_1658_0_0_nb.cyacd, it is okay to let CCG3 work with FW1 and show FW2 is not valid.
b. If you only boot-loading CYPD3125-40LQXI_notebook_two_3_1_1658_0_0_nb.cyacd, it is okay to let CCG3 work with FW1 and show FW1 is not valid.
If the only one firmware is damaged, the CCG3 will stay bootloader mode.
A2: Refer above information.
A3: Yes. It is possible. You could refer CCG5 firmware architecture.
Hi Lisa san
Thank you for your reply.