First, my apology: I am not a user of OctoPrint or Raspberry Pi. I wanted to let everyone know that I have the same issue with a brand new Ender 5 Pro w/ 1.1.8 FW. Also, it doesn't matter if I print from Simpify3D, Pronterface, or the SD card: in all cases I randomly lose the Y axis. Just like all of you, my Y motor seems to be disconnected, because I can move it with very little resistance.
I have gotten a couple of good prints, including the owl that came with the printer.
One other thing I found. When I tried to print 3DBenchy, it came out half height. I tried again and got the same result. So, I scaled the X axis only, and got a 'not too bad' Benchy.
Through Internet research I discovered that it was possible my Z stepper motor steps/mm may be off. It was @ 400, so I changed it to 800, and suddenly my prints are full height. I realize this not strictly on-topic (I apologize for that) but I thought it might be useful to at least 1 person in this thread.