I’ve been working on a project for a little while and I’m unsure which is the better architecture. I’m interested in the consensus. The answer to me seems fairly obvious but something about it is digging at me and I can't pick out what.

The TL;DR is: how do you handle a program with application data and user data in the same DB which needs to be able to receive updates to the application data periodically? One database for user data and one for application, or both in one?

The detailed version is.. if an application has a database which needs to maintain application data AND user data, and the user data all references application data, it feels more natural to me to store them in the same database.

But if there exists a need to be able to update the application data within this database periodically, should this be stripped into two databases so that one can simply download the updated application data database file as an update and replace the old one? Or should they remain as one database, and the application data be updated via a script which inserts the new data into the existing database? The second sounds clearly preferable to me... but for some reason just doesn’t feel right, and I can't pick out quite why.