[CentOS] lost connection during yum update

During today's big Centos 6 update I lost my connection to a machine during the "yum update" and when I logged back in and ran yum update again it told me to run yum-complete-transaction. When I ran yum-complete-transaction I got screen after screen of "x is a duplicate with x" where x consists of a huge list of packages.

"package-cleanup --dupes" gives me a huge list of packages.

I think that my next step here should be "package-cleanup --cleandupes" but when I do that it tells me that it will remove 800-plus mb of files. I suppose it's the the same list that I get with "package-cleanup --dupes".

Do I want to do this or will that nuke the operating system? If not, what should I be doing?