Similar to the behavior of this Upgrading WP to 5.0.1 deletes civicrm uploads folder, I had deactivated then decided to delete a site on our WP multisite. Once I clicked delete I got a fatal error (sorry I did not copy) that referenced line 916 of civicrm.php file. Deactivating CiviCRM plugin got the multisite backup.
require_once 'CRM/Core/ClassLoader.php'; CRM_Core_ClassLoader::singleton()->register();
Then I saw that the uploads/civicrm folder was empty. It had the /ext /uploads and /template_c folder but they were all empty. The rest were gone.
We restored the directory from backup and now it works. Anyways, this is a word of caution.
Question is, why did this happen?