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From my experience*, using a subfolder structure will yield the best results. I think the more important factor is how these pages are linked to from within other pages on your website. You need to build links from high authority internal pages to your degree pages using keyword rich anchor text. If you do this from both websites, I don't think it will make much of a difference which domain the pages are hosted on. i.e. if you link to the degree pages sitewide from both domains, you will see similar results hosting them on either domain. So if you are going to move the degrees to the other domain, you might as well switch to a subfolder structure. If not, focus on building a stronger internal link profile. *As you said, this topic is highly debated. Google's official stance is that there is no difference for ranking between subfolder/subdirectory. They also say that if the content on the subdomain is highly relevant to the content on the root domain, they will be treated as the same domain (authority overflows).

I am not sure there is an easy answer. I would calculate your losses on the de-indexation I would OSE the URL's in question (and verify through webmaster tools) See how many external sites point to them. If you do not have many incoming links, then I am not sure de-indexation is so bad, comparatively to the man hours or work needed to keep this up now and in the future. I think it would just become almost like a Profit and Loss (P&L) scenario. Also if you are already seeing duplicate content penalty's, in the grand scheme it may help to get rid of those pages as post PANDA it MIGHT be dragging you down. But really this is all speculation, as I am not fully "up to speed" with the exact situation, and the answer in my opinion would be based on alot of factors not just SEO. Hope this helps! Shane

We're working on it!

Hi Kristina - sorry for the long delay! I definitely wouldn't go with sub.subdomain.rootdomain.edu - I'd go with a subfolder and hopefully, something as close to the root/main domain as possible.