There is a simple way to change package, please refer: How to change package on S32DS Processor Expert
Different package will not impact the wake up function, please direct download that example and then change package to test.
Please first make sure the example works on your board.

I have tried to flash the "Example S32K116 FlexCAN PN STOP S32DS.ARM.2.2" into S32K116EVB, it was able to work when powered by 12V power source(J107 1-2).(Without external J-Link debugger connected)
Best Regards,
Robin
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