Arduino Micro serial communication is not working after wake from power down
I found the answer on this related question: Starting usb on pro micro after deep sleep (ATmega32u4)

Which itself was a link to a sparkfun forum

Note: it requires you to close and open the serial monitor at proper timings.

// disable the USB prior going to sleep
USBCON |= _BV(FRZCLK);  //freeze USB clock
PLLCSR &amp;= ~_BV(PLLE);   // turn off USB PLL
USBCON &amp;= ~_BV(USBE);   // disable USB

// and wake it up after
//routine to properly wake up
sleep_disable();
delay(100);
USBDevice.attach(); // keep this
delay(100);
Serial.begin(9600);
delay(100);