Hmm they are supposed to update.. but you can try deleting the nameofyourscript.pex file in steam → steamapps → common → skyrim → data → scripts
Should that not work, then you can delete the nameofyourscript.psc in → scripts → source
It will be removed from the CK entirely. Back it up first, and then create it again.
This is weird though..it's supposed to update in the CK...