Moving drupal site to the root of the server
I guess you can upload the new .htaccess file and change back the line #RewriteBase if you have modified only one line of the .htaccess file, there won't be any problem and even if the file exists there it will give you a option to replace.

Few things that you have remember while moving your site to root folder are:


Put the site into maintenance mode so that user's posts, comments etc. doesn't gets lost.
The #RewriteBase is uncommented when we use the drupal from the subdirectory. So if you are moving it to the root folder than I guess no need to modify this line. (Anyways you try you way also).
If you have modified/using the $base_url in setting.php than don't forget it to update as well.log
Clear the complete cache, and check the watchdog table data (dblog) at "/admin/reports/dblog" to make no page or anything is having issue.