Please make sure that you first unzip the Theme file you downloaded from Theme Forrest and inside that zip, you will find some instructions as well as a second zip file. That second zip file is the one you need to upload.
You know, that is a really good question. I always use SSH or sftp to add, update or delete themes or plugins so I never have to worry about missing files or security issues. But yes, you would have to either (a) delete the theme first (which will make you lose settings and customizations made to templates and then install the updated version of the theme. or (b) use FileZilla to delete the theme without touching the custom.css file (and don't even deactivating the theme on front end) and quickly transfer the updated files.
***Please make sure you first do a complete database backup as well as have a spare copy of the original theme's files prior to deleting them
in case anything goes wrong.