How to upload a fresh set of files From Online Manual

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When the database is OK, but some SMF files are damaged, it may be a good idea to reinstall the current version of SMF. This recreates what is called a "clean SMF installation". This might be necessary if

  • a mod fails to uninstall, leaving the forum unworkable
  • SMF upgrade fails because of the changes mods have made.

These are instructions to restore the current version of SMF, without making any changes to the database. Then, it will be possible to re-install mods or upgrade to a newer version of SMF. These instructions will delete all mods and themes, and erase all hand-made customizations from php files. For other options, please seek support at the 1.1 support board or the 2.0 support board.

First -- Backup everything
Backup your database. Make sure you have backed up all your data!
Backup your custom themes and graphics. Make careful notes about any hand-made customizations you have made to files.
Download the large upgrade package for the version of SMF that you're using from the download site
Extract the package and delete upgrade.php and all the upgrade-x.x.sql files. If you leave the upgrade-x.x.sql files they won't cause any harm, as they can not be run without the upgrade.php script. But, it'll save a bit of space on your server.
Upload the files, EXCEPT UPGRADE.PHP (and the .SQL files), to the forum's directory, overwriting what's there, now. You can either use FTP or, at a pinch, CPanel's File Manager. On your forum, if you've replaced the standard smiley files with your own and/or replaced the standard avatar files, you might want to refrain from uploading the 'Smileys' directory and the 'avatars' directory.

Once done, your forum will be in a virgin state, software-wise. All of your members, posts, etc. will be intact. However, none of your mods will be installed, now. They will, fortunately, still be in Package Manager. From there, you can either apply/install them, or delete them, as you desire. Any of your mod's settings that are stored in the database will be retained and still be usable when the mod is reinstalled.