I think I may have found a temporary fix to my problem ...
Congratulations.
Just in case someone else someday runs into the same or equivalent problem, and while it is still fresh in your mind, could you give a very short description of what you uncovered, please?
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If you want to wait a few days for validation, that makes sense. However, I do suggest jotting notes down now. It is amazing how fast little details can fade from memory.
Probably best to wait a while to really confirm really what was causing it. Since I don't know for sure if my temporary fix or it's more permanent solution will work. So I don't know for sure the follow to be true.
However the reason for the entire system slowly crashing, while still kind of working, was the usb stick was becoming undetectable, either by becoming unmounted or ejected, as soon as any of the CM1's was connected via usb. I use a wireless mouse (usb bluetooth) and usb thumb drive since the beginning, it has always been that way, but this most recent problem only effect the thumb drive. I even tested if it temporarily effected the mouse and it did not.
Only programs which was entirely in memory continued to work, anything currently being access form the stick, disappeared. This lead to a slow but eventual system crash as more and more programs realised some quicker than others than it could not access it's files.
Debian has more system level and diagnostic programs installed by default that work entirely in memory, that were easy to find out how and what occurred and to get it working again. Btw I don't recommend ever yanking out a usb in mid-use, it's more obvious now how many orphaned files it has, while it didn't cause any permanent damage, I'd bet it would eventually.
While I've made only minor hardware changes since I got the system (Replacing a usb hub), nothing has changed recently, they did not coincide with the timing of this problem, it was a software change that allowed me to uncover this problem.
Getting a new powered usb hub. Gone through 2 since I got it, it also worked fine without them too for a while, connecting directly to the usb ports on the board, actually was most stable with it, surprisingly.
Hence while I'm uncertain if it will actually fix it, but I figured if the thumb drive could drop like that, only thing that could make it do that is a lack of power to maintain it, according to what little log info I have, it's not a software call or command that issued it.