I have Joplin sync through Dropbox (encrypted as well) on a Win10 laptop (which I can't access now) and Android phone, they're both sync well.
I installed Joplin on a new Win10 laptop, activated Dropbox sync and encryption.
I run synchronization, it runs, completed, and stops. Having fetched nothing at all...
It's hard to know what went wrong in situations like this, more so when the user is distressed.
Secondly, if I were you, in any moment of a doubt, I'd make some sort of backup from last correctly synced device.
Got data in Dropbox? copy that
Any data on old devices? disable sync and make a .jex backup
If there's android phone with root, attempt to save the database and data (more on that topic).
Once you made a backup, it should be a matter of its correct import. For example, if it's cloud Dropbox data, you may load it to other cloud, sync it to a device with clean Joplin profile.
There's other good response about fairly similar problem:
I'm lucky enough I've been enough to export a .jex file from my original laptop (which I thought was dying).
But now that I've imported it on a clean install of Joplin, all my attachements files are in conflicts too!
I'll have to manually copy/paste each picture in each note... what a mess...
If you've got a correct .jex backup, you can change the sync cloud to avoid conflicts:
point a clean Joplin install to new cloud (not Dropbox, say OneDrive)
import the mentioned .jex to the clean Joplin installation
After making sure the import is complete and syncing fine, you may want to clean your other devices and sync them to the new cloud
About your initial question:
Why are there conflicts and duplicates when you import .jex backup to the cloud synced installation?
Joplin treats .jex import as new notes. So, importing .jex to clean installation and attempting to sync to old cloud (DropBox in your case) tells sync engine that there are no more old notes, only imported new ones.
The sync engine guesses that they might be the same and asks you to sort it out by marking them as conflict. To avoid it, it's best to import the .jex backup to a clean cloud. But not to mess up even more data, I suggest to start with a different cloud and resync all other devices.