Octopi + RPi0 + MK3S+ = no more serial connection  

Question

I am not sure of the answer to your question, but I have one of my own.  

How hard was the Atomic Pi to set up?  

Atomic Pi Setup difficulty rating.

It was more difficult to set up than a Raspberry Pi, because there's no "download and run" script.  But not much more difficult.  Instead of starting with nothing and ending up with a Debian/Raspian OS with OctoPrint  - OctoPi, you have to install and configure everything manually.  Here's a link to the process.  Note that is says "Not for the faint of heart."  I wouldn't say it's as hard as that message indicates.
https://community.octoprint.org/t/setting-up-octoprint-on-a-raspberry-pi-running-raspbian-or-raspberry-pi-os/2337

If you understand what SSH, git, the difference between an user and a admin are, then you should be able to breeze through the process.  I'd rate the difficulty of installing OctoPi a 1 out of 5, installing OctoPrint manually a 2 out of 5, and creating a custom Yocto or Buildroot based Distribution a 5 out of 5.

RPi Zero is not supported, I wouldn't bother

Posted by: @rob-w5

[...] One thing I'm REALLY confused about is the Setting RPi [off]/[on].  It seems to me that the setting is inverse of what it should be. 

ON is if you have a RPi wired in via GPIO rather than via USB. 

Regardless, neither option after restarts of both the Pi and Printer with the RPi set to either state don't allow a connection.  There was a short time where I had a connection today, but it turned back off in a few seconds.

Is it possible either the RPi or printer controller has been damaged?

So, I'm curious what the logic is in having the RPi set to OFF when you want to use one, and ON when you don't want the Pi to connect? 

If OFF you can connect via USB normally. Not sure why you're seeing different behavior.

And if there's any recommendation other than to use an RPi4 or another Atomic Pi in place of the Pi0.  Any way to bring the existing and once functional setup back to life?  I'm current on all firmware/software other than the Pi0 running Ubuntu 18, not 20.

No, no other recommendation. The RPi Zero is very cool, but the developer of OctoPrint specifically states that it is not suitable nor will the developers spend time trying to ensure future versions of OctoPrint will work on the RPi Zero. The cautions are more than "just don't use video". Notes here. I personally would not waste any more time using a RPi Zero with OctoPrint.

I found the thread, now to start tugging on it

I started looking at the log files of both the Atomic Pi (working fine) and the RPi0 (not working).  I've never poked in the corners of serial communication on the working system, I was only looking at the information I had in the non-working instance.  In the Communication Block, it has Device and Speed selected to Auto.  Clicking them shows AUTO only on the RPi0, and 33 different /dev/tty* devices on the AtomicPi.  Ah-HA!  Somehow, the list of serial port candidates has been deleted!  I put them back in using "Additional Serial Ports" in settings.  Now the Pi tests each port, but gets permission errors.  I checked to make sure all USERS in the RPi are members of the "dialout" group.  Which they are.  That should have fixed the issue, but hasn't.  I'm guessing that a profile or some critical files got deleted.  I'll probably have this figured out in another hour.
#bobstro, I will most likely change from the RPi0 to another AtomicPi or an RPi4 after I fix this.  But I really only use the RPi0 because I was able to integrate a camera on the printbed and everything looks so clean. Using the USB connection and a SBC not integrated into the printer will just be more clutter.  I am not in the practice of using OctoPrint to Print.  I use it to remotely monitor the prints via a camera.  (which I can still do with a broken serial connection.  Thus the long period of time between observing the problem and looking for a solution)

Thank you.

Thank you.  I might be something I might try.  

Posted by: @rob-w5

It was more difficult to set up than a Raspberry Pi, because there's no "download and run" script.  But not much more difficult.  Instead of starting with nothing and ending up with a Debian/Raspian OS with OctoPrint  - OctoPi, you have to install and configure everything manually.  Here's a link to the process.  Note that is says "Not for the faint of heart."  I wouldn't say it's as hard as that message indicates.
https://community.octoprint.org/t/setting-up-octoprint-on-a-raspberry-pi-running-raspbian-or-raspberry-pi-os/2337

If you understand what SSH, git, the difference between an user and a admin are, then you should be able to breeze through the process.  I'd rate the difficulty of installing OctoPi a 1 out of 5, installing OctoPrint manually a 2 out of 5, and creating a custom Yocto or Buildroot based Distribution a 5 out of 5.