Yes, and there is yet no good way to restart the USB Serial connection after sleep. I've tried various libraries (Adafruit has the best, I think) but none of them worked reliably in my tests.
Deep sleep and USB Serial on the SAMD are not yet compatible, so use an alternative hardware serial port instead, which will survive deep sleep. A Serial1 definition is built in the the Adafruit core and it is easy to define others.