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Its a common misunderstanding. Joplin files are .MD, and somewhere it says its markdown, because indeed Joplin uses markdown even inside the files.
But if you do open those files with any other markdown editor, you find out they are not plain markdown. The text itself is mixed up with other stuff (tags and such) in a non standard way. You notes are not lost and can be recovered, just not by straight open up in another markdown editor.