On a WordPress Multisite Installation I have installed Elementor and Elementor Pro. Both is not enabled for all sites. Trying to Elementor Pro update within the upgrade-feature of WordPress from Elementor Pro 2.8.3 to 2.8.4 did not work properly. Even trying to download Elementor Pro locally and reinstall it with upload feature did not work without removing the prior installation first, because the plugin directories did even exist.
After removing the Elementor Pro Plugin from the Multisite-Installation the new version of the Elementor Pro Plugin could be installed. No panic, all settings are still there.