Deploying the app (WordPress site) is different to transferring/syncing the actual data of the app.
I always treat the production data as the source of truth (this was mentioned somewhere here in a thread already).
When developing apps (which also WordPress site is), often staging/development data is used that should resemble real world data, so it doesn’t have to be necessarily exactly the same as on production.
An alternative to overwriting is syncing the data between servers (e.g. production and staging/development), see this thread Sync user (modified) content.