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I _believe_ (and I haven't tried this, so can't say for sure) that if you do a re-import of your books that LT will notice duplicates and will only modify things that have changed - like tags. That is, get the .csv file - maybe export your library? - fill in the ISBN (with your CueCat...though I'm not sure a clawed CueCat will translate correctly), put in the new tag(s) you want, and import again. You might try it with one or two books and see if it works first. The Help still says Universal Import only catches ISBNs, but it does get tags as well...I'm just not sure of the details.
Import page, with a sample .csv file for the new universal import.
Discussion of importing and link to blog announcement.
Hope this helps!