UPDATE: Looks like you answered that here already: https://news.ycombinator.com/item?id=49502025
If by mistake you actually have two separate instances of OpenRun pointing to the same S3 volume and path_prefix (with single-node Docker or with Kubernetes), the generated S3 paths have an binding ID which should be unique across instances. I will check whether there is anything more which can be done to prevent any issues with such an incorrect config.
Yes, it feels magical to just recreate your namespace or even create a new K8s cluster and see all your apps (from OpenRun metadata) and app data restored automatically.
SQLite is great for small-production scale. Don't let anyone tell you different. Just keep in mind that it's a pain to move if you ever do need to scale up. If it's a startup, you might. If it's a weekend hobby project you're building for your personal use only, you probably won't.