When you are debugging your application software using Nios® II IDE or Nios II Software Build Tools for Eclipse you may encounter this problem.
This is because while the execution is paused in debug mode, the processor does not stop the watchdog timer. This is a deliberate feature because in deployed systems, the watchdog timer should trigger even if the processor has hit a break instruction. Unfortunately the paused processor is not able to refresh the watchdog timer, so the watchdog timer resets the system and your debug connection is lost. To avoid this, do not enable watchdog timers while debugging.