Hi Paul,
Skyline doesn't have any way to track multiple CE values per precursor, so it just uses the last-seen entry when importing a library. There are probably many other machine values that would be interesting to track as well for the purposes of chromatogram extraction. We are actually working on tracking multiple ion mobility values, for instance.
Sorry I don't have a better answer for you.
Thanks for using the Skyline support board,
Brian Pratt