How unfortunate. I hope you can recover it. Just a thought. When one right-clicks a database in the left side Navigate sidebar, the “Delete” database option is nearby the “Close”. Sometimes when I’m in a hurry I mis-select, but if “Delete” is picked by accident there is a warning screen where one has to confirm the deletion and unless confirmed DEVONthink won’t delete. That usually wakes me up, but perhaps an inadvertent deletion occurred?
PS. I’ve often thought of putting in a change request to DEVONthink to move this Delete option all the way down to the bottom of the selection box, or even remove it since there is a Menu:File → Delete Database … available.