Deleted copies of notes deleted all files original and cloned

In that case @fallendaemon it seems you will still need to have a dig around in the database but it is at least easy to restore the notes once you find them.

(Sorry if anything here is obvious but it might be helpful to people in the future). You will need to open your Joplin database. In Joplin go to Help > Open Profile Directory and copy the database.sqlite somewhere. To open it you need some kind of sqlite browser of which there are many, sqlite studio is probably the easiest.

So, open the deleted_items table and go to the data tab and look for the various item_ids. You can then query them in revisions (just paste the id into the filter box) to make sure they are the correct ones (or don't and just restore a bunch then re-delete them later if not needed).

Open the command pallette (ctrl + p) and type restoreNoteRevision followed by the note_id e.g.
restoreNoteRevision 8066304e11c641428d001c1cdaffcb70
then hit return and it will tell you if it was successful.
Rinse and repeat for all your other notes.

There is also a guide by @theCollectiv if that makes better sense than my ramblings