This surprises me. I was under the impression that SQLite backups run inside a dedicated transaction in order to avoid this.
This comment cleared that up for me: VACUUM INTO backups are transactional, but the .backup mechanism is not: https://news.ycombinator.com/item?id=31387556
Ben I suggest updating that cron backups documentation page to recommend VACUUM INTO instead!
Could start an issue: https://github.com/benbjohnson/litestream.io/issues
Good catch. I went ahead and added an issue on the docs. https://github.com/benbjohnson/litestream.io/issues/56