Hello @Poley
I'm not sure if I got this right, so you are now able to flash the code over CAN? The issue was the "Serial" option selection?
Let me explain how the code generation behaves in our toolbox. When the download method is OpenSDA, the code will be generated with no appkey, and with the same linker file from the S32SDK. The code is built and if the "download code after build" option is checked it will flash the board by copying the .mot file on the board's mounted drive.
If the Serial option is checked, then in the generated code is inserted the appkey header and the linker file allocates space for keys as well. Now, if the "download code after build" is checked, then the toolbox will invoke the RappID Bootloader, but this will work only for the UART communication, so maybe this is the reason for that error you have attached. For CAN, you can uncheck the download option, and flash it as before.
Now, unfortunately, I don't have the experience for multiple targets connected to the same CAN bus for RappId Bootloader. @jiri_kral do you have any suggestions here?
Regards,
Marius