Capistrano Deploy Wipes Database?
Chances are you are using SQLite, and you are keeping the database in the default location. Your database is not being deleted, more just left behind.
You need to edit your database.yml and tell it to keep your production database in a shared location "../../shared/database.yml" or similar (you may be better off using an absolute path, or for bonus points MySQL).
When you deploy via capistrano it creates a new copy of your app in a timestamped directory. Your database is being left behind in the old timestamped dir.