How to upload a fresh set of files
From Online Manual
When a mod fails to uninstall, corrupts something it should not had or makes SMF unable to upgrade. Then the following instructions will help reset SMF, but preserve some important information like topics, posts and members. Warning, the following instructions deletes your currently installed mods and uploaded themes. If for any reason a different option might be available ask for support at the 1.1 support board or the 2.0 support board.
BACKUP ALL YOUR DATA!!!
Download the large upgrade package of your forums version.
Open the package and delete upgrade.php files.
Delete everything in the forums directory except for the settings.php file and the attachments and avatars directory.
Upload the package to the forums directory and unzip the files.