How to check whether application firmware ran sucessfully?

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Hi,

 

I am working with SAMD21. I've loaded the bootloader. In my application code, I'm setting a bit at the end of the code to inform the bootloader that the code ran successfully. In bootloader, I'm checking whether this bit is set, if it isnt then I return to the bootloader. But how do I check this? I removed certain bits from application code binary file. 

 

Thanks.