A small update:
Oh, I have an idea. Does Joplin require the folder it uses to be named Joplin? Can it be ex. Joplin-Debug? I want to create a fresh, small folder and not upset the main one 
@mic704b
I'm seeing sync conflicts, but most of this is because I caused conflicts by mixing webdav sync with nextcloud sync with the native client. I want to exclude those and make sure, that I'm not seeing some other conflicts.
Your actual database is usually stored in a “profile” directory called joplin-desktop, the location of it depends on your platform.
You can tell Joplin to use a different profile directory, using a --profile argument when you start it. I don’t know if it is officially supported, or exists on all platforms though.
That way you can experiment and not wreck your real data. Be careful though not to mix them up. (Always back up carefully.)
Hello everybody!
It's been a bit of a journey. I'm still not at the end, but it seems I'm making progress. 
A combination of a local issue and an obscure edge case will make your days an annoyance.
After trying and doing observations I decided to reinstall my entire OS and migrate only configuration for software that I'm 100% sure I want to migrate. Joplin's data was backed twofold:
~/.config/joplin-desktop folder*.jex archive of the entire Joplin installationThe first item was kept only for reference. I then proceeded to wipe my drive and install Ubuntu 18.04 on it (KDE Neon).
I created a folder ~/joplin/rel-test-2 for Joplin to use. This was to be synced with other nodes via Nextcloud.
I downloaded the Joplin appimage (1.0.197) and ran it, setting ~/joplin/rel-test-2 as a back-end (file-system back-end). I then proceeded to set encryption and prepare the second node (laptop) the same way. After testing that both nodes have the same data and that E2EE is working I loaded the *.jex archive onto one of the nodes (PC) and waited for the sync to complete (Joplin to disk, Nextcloud to cloud provider). I then powered on the laptop again and waited for the sync to complete here. I don't know why, but Joplin on the laptop couldn't detect the data to load. I recreated the .config/joplin-desktop folder and all went well.
I decided to keep track of potential file drift. I would every few hours create a debug report and also copy the contents of the Tools > Synchronisation Status page. I would put that on a separate drive for safekeeping.
After switching machines I'd use sort to make sure the entries are in alphabetical order (to help with using diff):
I would then use vimdiff file-a.sorted file-b.sorted and look for differences. Here is an example:
downloaded and decrypted) all would be the same.
This meant that whatever was causing the drift, died when when I reinstalled the OS. Come to think of it, sometimes after waking the PC from sleep, I'd hear two BIOS beeps. I read that this may mean memory issues, but there was nothing mentioned about waking the PC up from sleep vs. a cold boot. It's been a week since I reinstalled and despite using sleep all the time, there were no beeps.
After becoming more optimistic I sadly noticed once again that notes are getting sometimes reverted to a previous state. But there was no drift.
This suggests that sync drift and sudden reverting of data are separate issues with separate causes.
So I decided to switch from file-system sync to WebDAV sync using a method outlined here:
I'm keeping track of the data I input into Joplin, by keeping a copy in a separate place so I can compare and look if anything is missing. So far I haven't noticed anything vanish. I'm giving myself some more days to observe the issue.
I remain optimistic.