I just found an issue with a server that wouldn't let me install any additional software with yum because it complained of an incomplete transaction. Plus checking the list of installed RPMs with rpm -qa showed that many of them where duplicated (old and new versions at the same time).

I used the following commands to get out that mess, and worked beautifully :

package-cleanup --dupes | grep -v Loaded | grep x86_64 | awk 'NR % 2 == 0' | xargs -n1 rpm -e --nodeps --justdb --noscripts
package-cleanup --dupes | grep -v Loaded | grep i686   | awk 'NR % 2 == 0' | xargs -n1 rpm -e --nodeps --justdb --noscripts
package-cleanup --dupes | grep -v Loaded | grep noarch | awk 'NR % 2 == 0' | xargs -n1 rpm -e --nodeps --justdb --noscripts
yum update
yum-complete-transaction
yum -y reinstall kernel

The first command is the meaty part; get a list of duplicate RPMs and, with the awk command get one out of two lines. Then pipe that list to rpm so we can mark the RPM as removed without running their removal scripts, or actually removing the files from disk !

After that, running yum update will take care of ensuring we didn't remove any dependency and finally yum-complete-transaction will replay the last failed command.

The last command is optional but apparently is a common problem to end up with a borked kernel and/or initrd, so reinstalling it for good measure.

As a sample of what yum and yum-complete-transaction where complaining about, here's a small excerpt of what was going on at the time of the issue:

--> Restarting Dependency Resolution with new changes. 
--> Running transaction check 
--> Finished Dependency Resolution 
Error: Trying to remove "systemd", which is protected 
Error: Trying to remove "yum", which is protected  
 You could try using --skip-broken to work around the problem   
** Found 43 pre-existing rpmdb problem(s), 'yum check' output follows: 
audit-libs-2.7.6-3.el7.i686 is a duplicate with audit-libs-2.6.5-3.el7.x86_64   
32:bind-license-9.9.4-50.el7.noarch is a duplicate with 32:bind-license-9.9.4-37.el7.noarch
7:device-mapper-1.02.140-8.el7.x86_64 is a duplicate with 7:device-mapper-1.02.135-1.el7.x86_64
7:device-mapper-libs-1.02.140-8.el7.x86_64 is a duplicate with 7:device-mapper-libs-1.02.135-1.el7.x86_64  
dracut-033-502.el7.x86_64 is a duplicate with dracut-033-463.el7.x86_64
e2fsprogs-libs-1.42.9-10.el7.x86_64 is a duplicate with e2fsprogs-libs-1.42.9-9.el7.x86_64  
fipscheck-lib-1.4.1-6.el7.x86_64 is a duplicate with fipscheck-lib-1.4.1-5.el7.x86_64  
glib2-2.50.3-3.el7.x86_64 is a duplicate with glib2-2.46.2-4.el7.x86_64
glibc-2.17-196.el7.i686 is a duplicate with glibc-2.17-157.el7.x86_64  
glibc-common-2.17-196.el7.x86_64 is a duplicate with glibc-common-2.17-157.el7.x86_64  
gobject-introspection-1.50.0-1.el7.x86_64 is a duplicate with gobject-introspection-1.42.0-1.el7.x86_64
kbd-misc-1.15.5-13.el7.noarch is a duplicate with kbd-misc-1.15.5-12.el7.noarch
kernel-tools-libs-3.10.0-693.el7.x86_64 is a duplicate with kernel-tools-libs-3.10.0-514.el7.x86_64
krb5-libs-1.15.1-8.el7.x86_64 is a duplicate with krb5-libs-1.14.1-26.el7.x86_64   
libblkid-2.23.2-43.el7.x86_64 is a duplicate with libblkid-2.23.2-33.el7.x86_64
libcap-2.22-9.el7.i686 is a duplicate with libcap-2.22-8.el7.x86_64
libcom_err-1.42.9-10.el7.x86_64 is a duplicate with libcom_err-1.42.9-9.el7.x86_64  
libcurl-7.29.0-42.el7.x86_64 is a duplicate with libcurl-7.29.0-35.el7.x86_64  
libdb-5.3.21-20.el7.i686 is a duplicate with libdb-5.3.21-19.el7.x86_64
libgcc-4.8.5-16.el7.i686 is a duplicate with libgcc-4.8.5-11.el7.x86_64

Happy hacking!