Use "rsync" instead of "cp". After it finishes copying, it will check to see if the file has changed since it started copying, and will restart the copy if so (with a limited number of retries).

If copying the entire database is faster than your average update right, this will converge very quickly and will deliver a consistent copy.

For many small applications, this is perfectly fine. It's not much harder to just "sqlite3 $file ".backup $backupfile"' (that's literally all it takes, and what you should do) and guarantee consistency. But it's nice to know that a simple "rsync" is sufficient for slowly-updating uses - e.g.

And as for the other side of backup, you know -- restore -- sqlite shines brighter than everything else. You can just take a good copy and put it back. You can examine the file everywhere, on a read only system, etc - without configuring anything if needed.