If you have at least one client device with up to date data, you can start from scratch from there. I recommend the linux desktop over the android device because the latter might not have downloaded all resources depending on your sync setup.
On your linux desktop, first export your data as JEX to be safe, then ignore it. Spawn a brand new joplin server. Sync your desktop to it. Reset all your other devices (either uninstall and reinstall the app, or create a new profile) then sync them to your server. If you do not reset your devices first, you will duplicate your dataset.
In my experience it's much easier to start over from any clean client device than from a broken server.
Good luck! 
By the way, a useful guide for starting over: How to fix synchronisation issues and start over