Staging multisite recommendations

I have a live multisite and I need to apply changes on it and I would like to know which would be the best process to not lose any new update(s) that were added to the live site while I was working on the changes on the staging site.

So I would like to know how to keep all the new changes applied to the production site (new comments, posts and so on) that were added while I was working on the staging site before pushing it live. And also how do this effectively for each subsite for which I am applying changes on the staging site and how to keep it organized for each subsite.