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I understand your concern--sometimes you don't want to mess with things that are working. But if it is clear to you that the sites need to be separate, then they need to be separate. When you make a change like this, you will most likely see an impact on search, as Google tries to figure out what is what. Ultimately, the pages will do best on the site that is the most relevant.

Thanks Monica, seems the unrelated URL that is not being served is in the manage page grade section so I have removed this. Will the keyword & this URL (now deleted on the manage page grade section) then be updated as the URL is still showing related to the keyword in the keyword rankings section? Or will I have to wait?

Yeah, they should change it to ONLY give the archive option. That would be nice!! But yes, we just archive them all, just in case!

I would provide an example of one of the underperforming pages, and one of your pages that does well so we can analyze the differences and potential issues.