Serial port and Flash multiplexing

I have a 4200 board and need two serial ports. One port is duplex and I plan on putting that on serial port D. The other is simplex (only need to send) and thought about putting it on serial port C but read the warning that it was shared with the flash. It says that care must be taken when using this serial port. I am unsure what “care” might involve. I don’t specifically use the flash in my code although it is obviously used to store the program code.
The simplex device I am using is a motor controller so sending it random data could be very bad if not destructive.
Is there a chip select or something that is raised when the flash is accessed? Is the flash used in the background other than during initial RAM load and programming?