I tried to do this to alter/remove the Timed Crosshair Snapshot shortcut, because:
I don't want a shortcut for Timed Crosshair Snapshot The default shortcut conflicts with other applications (specifically Emacs)
I modified the shortcut in both Skitch and the Skitch Helper application as new Keyboard Shortcuts in System Preferencees.
I also verified that the shortcut overrides were taken by Skitch and Skitch Helper.
Even though the menu items show that there should be new shortcuts (⌃⌥⇧⌘5) for Timed Crosshair Snapshot, they don't work. The default shortcut (⌃⇧⌘5) still takes precedence and conflicts with Emacs.