Messed up media library

You can batch upload using SFTP and then use the plugin “add from server” to add those images to the media library.

will that actually replace the images on the site with the new ones automatically?

As long as the images have the same file names and are uploaded to the same directories, you won’t need to change anything in your site’s content.

And if you overwrite the files, you should not need the add from server plugin.