What is the correct methodology for applying new versions of change sets?

eg. I had filed in the CrispScrollBars change set before applying the 
latest Updates, now the same change set is included in the latest 
Updates as CrispScrollBars2 with some tweaks. Is it safe to remove 
the first version after the second is filed in or should it be 
removed before the new version is applied?
    Thx.
    Ken