Nevermind I finally figured it out the problem, basically, by comparing the files with my backup I noticed that the file /etc/httpd/conf.d/~lxcenter.conf was missing, which contains the includes for the domain config files right?
so I just run sh /script/apache-optimize and the file ~lxcenter.conf was generated!
Finally looks like everything is working fine as it was before, I apologize for being a pain in the but! Thanks for the support Mustafa for the support. I will try to donate you something, being a long time user of Kloxo it's only fair.