Sometimes the failsafes on a system can get in the way of reconstructing things after a boo boo. For example, if you try and re-install a package over itself after accidentally removing a file -- yum won't let you. However it is relatively easy to recover if you know how.
The first step of course is determining which packages may have been damaged. To verify a package use rpm -V, and possibly --nomtime to avoid showing when files were modified, e.g.
rpm -V --nomtime packageName
Where packageName is the name of the package. To verify all packages on your system use something like this:
rpm -qa | xargs -t -n1 -ipName rpm -V --nomtime pName
Or, if you're looking for any damaged packages in a set of related packages you can do something like this:
rpm -qa | grep partOfPackageName | \
xargs -n1 -i pName rpm -V --nomtime pName
Where partOfPackageName is part of the package name.
Once you know the packages that need fixing, you can "remove" the package from the rpm db so that yum thinks it is no longer installed and re-install with yum, like this:
rpm -e --justdb --nodeps --allmatches packageName
yum install packageName
where packageName is the name of the package. Once yum finishes installing the missing files or other problems should be fixed.
Note: if somehow you've damaged your rpm database, perform these steps to recover it:
rm -f /var/lib/rpm/__db*
rpm --rebuilddb