Hi rahul,
1. Debugging when COP watchdog is enabled is quite tricky. You probably cannot use stepping over code because stepping takes longer time than COP timeout. You could set COPCTL_RSBCK bit for Stops the COP and RTI counters whenever the part is in Active BDM mode, but I am afraid that it will not help you so much. For debugging COP reset, you could use indirect methods like LEDs, triggers and trace (trace buffer is not affected by COP reset). For more details, please see "c:\Program Files (x86)\Freescale\CWS12v5.1\Help\PDF\Debugger_HC12.pdf" document.
Are you really sure that it is really COP who invoked MCU reset?
2. We do not know about any direct connection between CAN and reset. So, there must be probably some other issue like illegal address reset, endless loop – COP timeout, low voltage reset,…
Semaphores have to be used for access to shared memory or shared peripheral between CPU and XGATE.
3. Reset sources are described in Table 1-13. Reset Sources and Vector Locations in RM.

I hope it helps you.
Have a great day,
RadekS
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