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We make software, and are moving from a horribly unoptimized site to a gradually more optimized one. We have inbound links coming mostly to foo.bar.com at the moment, for two reasons:
1. shortness ("viral marketing"),
2. an URL that stays valid even if the site structure shuffles around.
Meanwhile, the site's internal links (and thus affect on PageRank) are in the form www.co.com/product.
Is the detriment to PageRank severe enough that we should change inbound links to www.co.com/product? Or perhaps change internal links to product.co.com?
Apologies if this has been discussed before. I spent nearly an hour looking for it, but no luck.
If they have also inbound links from other websites it would be nice if the backlinks and the incoming links are equal.
I would recommend to change your backlinks because they are under your control.
<edit> Or do you mean that you have independent sites with index pages for the products? </edit>