As far as I can tell, Open Site Explorer doesn't show all the links - in fact it shows only a very tiny proportion of the links to your site. Yahoo site Explorer, while it's still available, is a more accurate list of links to your site. For example on our little site, OSE shows 30 in bound links, but Yahoo shows almost 300!! As painful as it may be, I would 301 every page, but do them in SE Rank order, it only has to be done once, and when it's done it's done. That said, I'm surprised your web company can't find a way to automate it?!
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RE: 301ing entire E-Com website - Using TopPages Report as a Guide