I was thinking about a good time to do this, as I don't want to apply it and it cause some downtime while we change the index.template.php.
Looking at the error message, I think the only changes it wasn't able to apply was to index.template.php, so I should be able to upload it here, then when changes are applied, I can upload the new version, and then apply the changes? I know I'll still get the error, but the changes will have already been made. Is that correct?