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...
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.