I was working on a WP + WooCommerce website (shop + blog), very active site - a lot of orders, users and posts. I was working with some plugins (settings), installing new plugins, removing old ones and even did some custom coding.

All the changes were performed on a "cloned" website, migrated to a maintenance subdomain. Now the changes are done. What is the best way to migrate the site to its main domain, without losing anything? Because in the meantime plenty of new articles and orders were posted, also a lot of users registered, etc. I need the posts and orders to remain the same (IDs and everything), but I want my changes to apply.

Basically, everything related to code and WP settings needs to be overwritten by my changes, and everything posted to the site (it's content) needs to be the same.