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Hey Ryan, Thanks for your response! Yes, that makes sense. I will give it a go! Thanks for your help! J

Hi Matt-Antonino, Great - thank you. Ok, I'm glad it's not going to be a problem! Thanks again, J

Hi! I had the luck to talk with a joomla developer and he gave me a solution that sounds too easy for me. The duplication is generated by the categories.  Therefore we set up all the menu items like index, follow and categories like no index no follow. He said it works perfectly for him. I cant believe it is so easy. I will make a trial and let you know if that solves it.