Upload fresh WP in site with w

Current wp install in directory and operating as root.

This install seems a bit buggy, so I want to upload a fresh WP and create a new database and run the new install from root, as I usually do.

Question is the other install? Can I just remove wp-config, and index and htaccess from root and keep the old files in the directory they are in?

Will WP get confused even if this is new with new database?

I want to do this today so any help is greatly appreciated.