They way I do update my all blogs is via IWP dashboard.
The ideea is that in WP, by default, contributors are not allowed to upload images. So this is the exact reason I installed URE. I allowed the Contributor via URE capabilities to be able to upload his images and all works fine. Until I update the plugin. Any time.
So it is a settings keeping issue, as long as other plugins (which of course have their own settings) are keeping their settings fine after any update.