A SQLite db is just a file isn't it? So you can use your normal backup capabilities to do it.
For example, I have some BASH scripts that do daily, weekly, monthly backups of my whole node-red installation. Using links to keep the size to a minimum (and not backing up the node_modules folders which are easily replaced with a npm install). These run on CRON schedules so that I don't have to think about them.
Just copying the file won't work because the database index get corrupted.
I'm using an exec node with the settings as show below. with the sqlite backup command.
This will make a backup of the sqlite database. This will lock the sqlite dbase temporary to make a backup.
You can trigger the exec node (daily) with the trigger node.