I found this out the hard way. I was trying to setup booting of Sata SSD but could not see anything on the pc terminal I found the system booted better without the jumper on J18 so I had removed it early on. Once I had my pc setup to monitor the CN6 port I was not getting any data. I debugged everything else then I decided to put the jumper back on and see if anything changed. It did
It doesn't kill it, removing it connects the port to the Arduino Chip, so it can be flashed via USB, as stated in the documentation.
What I am saying is I got no data from Uboot with the Jumper off. So the Serial Port was not connected.