@Rob - I am not official staff at all but I also recently moved my whole print farm to RS and love it. Same scenario as you with several printers and I had to discover some fixes. Just ahead of the curve I'll tell you - it's worth it. RS is so much more stable and light-weight it's insane. A single RPi 2 (yes 2, not 3B or 4) is running 3 printers with 0 issues for 6 days and huge GCode files.

Anyway moving on --

I had and randomly have the issue(s) you describe primarily on printers running firmware that is older than Marline 2.0.x aka Marline 1.x like many printers do.

In my case there were a few things I did to drastically improve overall USB performance. It would be helpful if you could specify what NUC you have and how it connects - built in USB ports? How many are there? etc.

Anyway this article (it's for Raspberry but even if you use another NUC it applies): https://www.repetier-server.com/knowledgebase/undervoltage-and-throtteling-of-pi/ Take special note of the Solutions section where you void the "5v" line on USB adapters. If you ever noticed when you switch the printer off but it's connected to your NUC and the printer screen or some sensors stay on -- that is because it's leeching 5V. This can cause noise and dirty signals depending on the power source and is also just annoying - I suggest at first taping over the 5V line, this made my USB in general so much more stable on all my 3D Printers.

Next -- when setting up the printer under the USB Select the correct USB port listed (not the default one it picks, make sure to use a direct link to the tty/SO USB port) and also set the baud to 115200 for the Prusa MK3.

Make sure to pick the correct firmware type in the "Add Printer" options too and then test. If it throws an error change the firmware to something else, change it back to the correct and hit "retest", most of the time this will cause it to fix and jump to the next stage of testing just fine. Happens regularly to me and then works fine.

There are also a few versions of the Prusa stock firmware that have some buffer issues which cause problems, there is a forum post about it: https://forum.prusaprinters.org/forum/original-prusa-i3-mk3s-mk3-general-discussion-announcements-and-releases/octoprint-issues-and-tips/