Hi @goczilla
That's normal behaviour for a board that uses its native USB port to connect to your host computer. If the microcontroller goes to sleep, its USB module powers down and the COM port connection is lost. Waking up doesn't reestablish connection with the host's driver.
If you require the COM port connection to stay alive then it's necessary to use an intermediary processor/FTDI 3.3V USB-to-Serial board, connected to the SAMD21's Serial1 port and use that for debug instead.