Comment by simonw

The ".backup" mechanism is safe - it's directly copying the file with "cp" that doesn't work.

Here's how to use .backup:

    sqlite3 data.db ".backup 'backup.db'"

You can also do this:

   sqlite3 data.db 'VACUUM INTO "backup.db";'

That's slower, but results in a smaller backup file: https://www.sqlite.org/lang_vacuum.html