Currently, AFAIK, the best way to do it is (on desktop app) to open the note in an external editor, and find/replace [x] by [ ]. On the mobile app there's no way to do it, you have to uncheck each checkbox individually.
An « Uncheck all » command would be most welcome !
IMO such a functionality should be natively implemented in Joplin, not through a plugin, because it could be used a lot from the mobile app (I am thinking of things like a shopping list, etc.).
Thanks for the tips ! Both desktop and mobile search/replace work fine indeed, and it's a nice workaround until there is a « Check all / Uncheck all » button one day I hope.