Thanks for your idea @bedwardly-down
So I've tried to move the ".sync" directory to a another directory (on both desktop & cloud)
I've backed-up the ~/.config/joplin-desktop
I've updated Joplin to latest version (Jex export backup does not seem useful, as I've continued using the app on an Android phone and typed manually all differences)
Exited Nextcloud client
Configured Joplin app with the webdav option, url provided by nextcloud (with the extra /Joplin at the end)
Running the app on Linux Mint, through webdav connection : I had the same error.
FetchError: invalid response body at: https://nextcloud.MYWEBSITE.COM/remote.php/dav/files/USER/Joplin/.sync/version.txt reason: unexpected end of file
Reopening the app on Android & syncing recreates the .sync directory.
Then, trying to sync Joplin app from desktop, the error message is still the same as above.
I'm sure the sync still works : I have an Android and an iPhone, and sync between both devices work great.