Ok the description is a little vague.
I don't think a clean install will "fix it". I don't think an update would have anything affect as the kernel,kernel modules and firmwares should not be touched during an update. In all honesty unless you are wanting to update Linuxcnc, there shouldn't be a need to do an update, most updates are just minor fixes that really don't affect the way Linuxcnc operates. The biggest "security threat" to cnc machine is someone getting physical access, and it would be the machine it self I would be the most worried about, blood gets everywhere, it's hard to clean and the injured party may want to blame you. I only will have wifi on when transferring files to the cnc machine, other than that I disconnect wifi.
I think you maybe experiencing an issue similar to what is discussed in this thread. Which it would is not Linuxcnc related, it's the ethernet port going to sleep/shutting down, tho it should be tx\rx ing packets more or less continuously. Yes I know it's a direct connection from the Pi to the Mesa card and the thread mentions switches a few times.
forums.raspberrypi.com/viewtopic.php?t=305820
It seems to be somewhat random to which boards are affected but I haven't noticed this on my RPi400.
Tho it might be an idea to check the power supply for the Pi & the mesa card. But if ti was the mesa card "dropping out" you would get notifications.
