1. Export your Local folder (ie all the documents in your database) as a .geneious file and save it somewhere temporarily on your hard drive. You can use the Backup button to do this, but make sure you select “Export local folder”, not “Archive all local data…”.
2. Create a new, empty database folder, preferably on your local drive in your User folder. Call it something like “Geneious X.Y Data New” to distinguish it from your existing database (which will be called Geneious X.Y Data - the X and Y denote the version of Geneious).
3. In Geneious, set this folder as your data storage location under Tools→Preferences→General. Choose NOT to move your existing database to this location, but rather “Create an empty database at the new location”. This should show a new empty Local folder in Geneious. Then drag the .geneious file you saved in step 1 into here to recreate your database.