When upgrading a WP multisite to 5.0.1, it completely removed contents within the civicrm uploads directory. I then restored the folder from the backup and all worked.
But this is weird, does anyone know why this happens? Has it happened to anyone else? Not feeling secure to upgrade on production yet when I see things like this.
It makes you run a db upgrade for all sites on the network but that shouldn't have anything to do with the uploads folder.