Yes, you can unplug either the CN-16 or SkyScan GPS receivers from your scope after they have linked and the scope will retain the time-site information they provided.
If you replug in the GPS while the scope is still on, the scope may not successfully receive any information from the GPS. It will continue to use whatever time-site information it had in memory before the GPS was replugged.
Disconnecting the GPS will make the mount reset the presence of the GPS the next time mount power is cycled. Re-enable the GPS by going to MENU > UTILITIES > GPS ON-OFF when you turn on the mount again.