generally, it’s important that you work on a setup which is only dedicated to development. That’s usually on your own computer, with a local database and the persistent data (in Data/Persistent). When you developed a new feature, you will check in your code to Git and deploy the code to the live website. Ideally you are using some kind of continuous integration tool (like Jenkins or Gitlab CI), but a git pull and composer install on the live server may also do for small projects which don’t mind a little bit of downtime.
That way you should never have a conflict with your development data and the production data. Once in a while you copy the database and files from production to your local machine, so you have some proper content to work with. And that should be it!