Thank you for the advices. I have opted for option a), the re-installation, due the problems with the removal of rpms. Just for the info, after successful restore, everything is fine and normal.
I'm not sure what command I have issued to upgrade the Samba packages, but I'm positive that the packages were from the SOGo repository. It was my mistake, since in the wiki the SOGo upgrade command is clearly stated. Might be that I have just enabled SOGo repo and just made yum upgrade, but I can't confirm it.
Thank you once again for the help and the advice.