Eu tive um problema semelhante e usei as etapas a seguir:
$ sudo yum update --skip-broke
$ sudo yum remove epel-release.noarch
$ sudo yum update
NOTA: pode ser necessário remover outros repositórios conflitantes.
Estou tentando instalar o skype versão 4.3.0.37 e ele continua me dando este erro:
Protected multilib versions: libwayland-server-1.2.0-3.fc20.i686 != libwayland-server-1.5.0-4.el7.nux.x86_64
Error: Protected multilib versions: json-c-0.11-6.fc20.i686 != json-c-0.11-3.fc20.x86_64
Error: Protected multilib versions: audit-libs-2.4-2.fc20.i686 != audit-libs-2.3.2-1.fc20.x86_64
Error: Protected multilib versions: libwayland-client-1.2.0-3.fc20.i686 != libwayland-client-1.5.0-4.el7.nux.x86_64
Error: Protected multilib versions: libpciaccess-0.13.3-0.1.fc20.i686 != libpciaccess-0.13.1-4.fc20.x86_64
Error: Protected multilib versions: libwebp-0.3.1-3.fc20.i686 != libwebp-0.3.1-2.fc20.x86_64
Error: Protected multilib versions: mesa-libgbm-10.1.5-1.20140607.fc20.i686 != mesa-libgbm-9.2.3-1.20131114.fc20.x86_64
Error: Protected multilib versions: krb5-libs-1.11.5-11.fc20.i686 != krb5-libs-1.11.3-33.fc20.x86_64
Error: Protected multilib versions: mesa-libEGL-10.1.5-1.20140607.fc20.i686 != mesa-libEGL-9.2.3-1.20131114.fc20.x86_64
Error: Protected multilib versions: keyutils-libs-1.5.9-1.fc20.i686 != keyutils-libs-1.5.8-1.fc20.x86_64
Error: Protected multilib versions: pixman-0.30.0-5.fc20.i686 != pixman-0.30.0-3.fc20.x86_64
Error: Protected multilib versions: 1:openssl-libs-1.0.1e-40.fc20.i686 != 1:openssl-libs-1.0.1e-30.fc20.x86_64
Error: Protected multilib versions: libtiff-4.0.3-15.fc20.i686 != libtiff-4.0.3-12.fc20.x86_64
Error: Protected multilib versions: systemd-libs-208-22.fc20.i686 != systemd-libs-208-9.fc20.x86_64
Error: Protected multilib versions: jbigkit-libs-2.0-10.fc20.i686 != jbigkit-libs-2.0-9.fc20.x86_64
Error: Protected multilib versions: libdrm-2.4.54-1.fc20.i686 != libdrm-2.4.47-1.fc20.x86_64
Error: Protected multilib versions: mesa-libGL-10.1.5-1.20140607.fc20.i686 != mesa-libGL-9.2.3-1.20131114.fc20.x86_64
Error: Protected multilib versions: pulseaudio-libs-5.0-7.fc20.i686 != pulseaudio-libs-4.0-8.gitf81e3.fc20.x86_64
Error: Protected multilib versions: libuuid-2.24.2-1.fc20.i686 != libuuid-2.24-2.fc20.x86_64
Error: Protected multilib versions: libthai-0.1.20-1.fc20.i686 != libthai-0.1.19-2.fc20.x86_64
Alguém se deparou com este erro e corrigiu-o?