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no. the rewrite rule will apply to all URLs

Here are my suggestions While upgrading software is typically a good thing, it sounds like you're possibly going to break things by doing it (I would assume we're talking major version changes, not patch levels). I would make sure of what you're going to break before doing it. At least make a test copy somewhere and monkey with it there. NEVER "tinker" with your live site. There are scripts that can export Joomla sites. If you do switch software, be meticulous in your 301s or take a ranking bath. Canonical your site. That will fix the duplicate problem easily. Why Wordpress? Consider a forum instead. A forum invites conversation and natively creates fresh content.

Thanks EGOL, that's in line with what I thought.  One of them does produce a small flow of visitors.  My inclination is to recommend editing the content on that satellite to reflect its keyword and only link in to the couple of relevant sub categories at the main site.  All other non relevant content would be removed The others I would redirect to the appropriate internal page of the website. All the best and thanks again.