Just a quick note: I deleted an inactive plugin from two sites. The UI here is not very clear, since about 30 seconds after deletion the display switches back to the default "update available" view, and clicking on "update all" after having deleted the plugin gets an " We detected an error" warning (see screenshots).
(Additional small rant: taking screenshots for Advanced Safe Update before updating inactive plugins might be unnecessary, no?)
I'm aware this might get fixed in an upcoming Umbrella UI, just wanted to document this.