Starting usb on pro micro after deep sleep (ATmega32u4)
I found an answer to a similar question here:
https://forum.sparkfun.com/viewtopic.php?f=32&amp;t=39214&amp;start=15#p175098

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);