A simple AppleScript to uncheck "show as run destination" for every device. Open the Devices window first.

ClearRunDestinations.applescript

activate application "Xcode"
tell application "System Events"
	tell process "Xcode"
		tell window "Devices"
			set deviceList to outline 1 of scroll area 1 of splitter group 1 of group 1
			set details to scroll area 1 of splitter group 1 of splitter group 1 of group 1
			repeat with r in row of deviceList
				select r
				-- Uncheck all "Show as run destination" boxes
				tell checkbox 1 of details to if value is 1 then click
			end repeat
		end tell
	end tell
end tell