I just delete the cache, vendor and phpbb folder from my server, and then upload all new files except the config.php
and .htaccess (have some edits in there). You can upload ext, images, store etc without problem, the don't overright your images, extensions etc... because those images, store... folders are empty.
BUT ALWAYS MAKE A BACKUP!
When you do style edits, it's better to create a "child" style, and make your edits in that style.
Also see: viewtopic.php?t=2492766