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I think. It is OK to turn it off while debugging since numerous print statements, stepping through code/VIs etc will sometimes trigger it.
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This issue(I believe) was about the system watchdog, which is a part of the firmware and cannot be easily disabled. That said, while disabling the "user" watchdog is sometimes needed for debugging, one needs to keep in mind that disabling this means turning off the primary safety system on the robot. Especcially when you can specifically see that the Watchdog is dying, you should be very cautious when running the robot without it enabled.