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This may not be what you're looking for but I would do as follows:

  • create a 2nd copy of your JEX file (all notes), just to be extra safe
  • uninstall Joplin from the desktop, manually delete the profile folder if necessary
  • manually remove the complete Joplin folder from your sync target (use a browser for this)
  • recreate an empty folder on the sync target
  • reinstall Joplin on your desktop, and import the JEX file
  • check notes to see you're happy with what you see
    IF desired
  • goto settings in Joplin and set up the sync target again (it's no longer there as we removed the profile folder !)
  • sync

Unless I misunderstood your description, that should do it. In any case, this way nothing can get lost ASSUMING that your JEX file was recent and complete.

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