How to maintain development losing any user’s data

Good practices.

When you pushing staging version to production environment, you do this though revision control system to update your files. When you need to update database structure, you use database migrations.

This means you have 2 different web-sites, that uses two different databases, or, at least, each web-site use it’s own table prefix.

Environment settings for WordPress are stored inside wp-config.php
You need different DB_NAME or $table_prefix