Ubuntu and USB connections get lost

We are using Ubuntu 16.04 on rasp 3 and the opensource plotter software ( OpenCPN).
It works fine, but the two connestions to the USB (/dev/ttyUSB0 and USB1) with different baudrate get lost after time to time.
The connection get lost after normal shutdown and after a “deep sleep” of the system as well.
Get lost means the connections are listed, but not working.
If I play around with the baudrates or reconnect the USB ports the system shows the data ( GPS and AIS).
What may be the reason the system forget the connections?

Thank you