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Sure, but (not actually knowing how the integrated controller works) I don't see why the hardware one couldn't do that too, especially since it seems to only be build to support CDC (serial) and JTAG.

Are you sure that the integrated one doesn't? It just seems like an odd thing to leave out.

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I'm not following, there is only one CPU: It has to run your application and 'operating system' (usb stack, Wifi if used).

Usually those MCUs don't have much memory protection, so when your app crashes down goes the whole thing. Writing UART is usually just writing data to a single register, fire and forget. This will still work if everything else is burning. (unless you screwed with the clocks)

Now USB on the other hand is a complex best, you have to keep state and do two way communication. If you corrupted your memory, you won't be able to get a debug message out over USB.

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