Going live with completed site

Hello all, quick question: I generally install WordPress into a folder of the same name (the default) when I am starting a new project. So, WordPress files sit in a folder that reads something like https://www.yoursite.com/wordpress. Okay, all well and good… the idea is to build the new site in that folder while the current site is still live.

Normally, once the new design is done, I would simply transfer all those files to the root directory and be good to go. But I have had some serious losses of work doing this. Is it as simple as moving files to the root and I have just screed it up, or is there another way to “go live.”

Thanks