We found the rascal responsible for the disappearing port! BRLTTY is a program that interfaces the Linux console with a refreshable braille display to provide accessibility for those with vision impairments. Unfortunately this program does not play nicely with other USB to serial devices like the CH340 chip on your Arduino board.
It seems there are several possible solutions to this, some of which are fairly complex. The most simple seems to be to simply uninstall BRLTTY, as described in this Adafruit tutorial:
Obviously this solution will be unacceptable if you use a braille display. Some other solutions are described here which should resolve the conflict between BRLTTY and your Arduino board without the loss of support for braille displays:
Another forum member who recently suffered from the same problem shared the specific solution they used successfully here: