EDIT: For paths to Plex SQLite and the database files on other platforms, see Repair a Corrupted Database.
On Windows 10, running Plex Media Server 64-bit. If still running PMS 32-bit, use Program Files (x86).
SQLite is picky with syntax. Note the semicolon at the end of the DELETE line and the period before quit.
This is a small database with no problems. Not sure if anything appears on-screen after issuing the DELETE command if something was actually deleted.
C:\>"C:\Program Files\Plex\Plex Media Server\Plex SQLite.exe" "%LOCALAPPDATA%\Plex Media Server\Plug-in Support\Databases\com.plexapp.plugins.library.db"
SQLite version 3.39.4 2022-09-29 15:55:41
Enter ".help" for usage hints.
sqlite> DELETE from external_metadata_items;
sqlite> .quit
C:\
Don’t download SQLite. Use the custom version installed with Plex Media Server.