If you only want to update one Application icon, ie, in App.app/Contents/Resources/App.icns
just touch the App.app folder. (I've read you need to do the Info.plist as well sometimes, although I've never needed to.)
Close the finder windows and:
touch /Applications/App.app
touch /Applications/App.app/Contents/Info.plist
You can refresh the dock icon cache using the commands above, also do a killall Dock
to restart it. Personally I would just drag the application in question, off the dock and re-start / keep in dock, because this is generally a one off thing. As always, script it if possible / and you're doing it a lot.
source: https://gist.github.com/fabiofl/5873100#gistcomment-1320553