As a follow up to this post, we launched the new site 3 weeks ago and seen a site-wide drop in SERPS
Of course there could be other variables involved, but we pushed ahead with the new product db without 301-ing the old products to new products as when we tried to do it, it was a far too time consuming exercise trying to pair up all the URLs in Excel.
Google has already indexed the new pages so hopefully the new site structure will not cause long term damage. In the mean time trying to 301 redirect as many of the best performing old product pages (as per Page Authority in the PRO crawl diagnostic tool).