It looks like the extlinux.conf plus serial console will keep the system happy as long as you pick the original boot entry.
Each serial console program has its own way of logging and setup. This is how you log. I use gtkTerm, and other than selecting my serial USB device being a pain, it is otherwise easy to use and log with. Unfortunately gtkterm does not understand the name of any serial device other than the older naming (like ttyS0…but not ttyUSB0) so you have to enter the device name on the host side by typing it in or saving it as a bookmark and editing the .gtktermrc file.
I am assuming you have a USB serial cable, and that the USB side is on your PC host, and the 9-pin D-Sub connector is on the Jetson. From your terminal program make sure speed is 115200, 8 bits, no parity, one stop bit. If flow control is listed you can try both CTS/RTS and “no” flow control. It sounds like the device name for the serial port is where the question comes in…assuming the USB side is on the host it’ll probably be a “/dev/ttyUSB#” where “#” starts at “0”. You won’t be using this information on the Jetson side because the 9-Pin connector is already wired for this…the Jetson side does not need to know about the ch341, only the host which is talking to the Jetson.
What serial console program are you using on the host side? I know minicom is very common, but it can be a real pain because it was designed to work with older modems which have an “AT” command language on top of the serial port.