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The answer probably revolves around your 301 redirects. I assume that you didn't keep the old URL structure. Was your site https before the change? Was it www? Did you have a trailing slash in the old URL? Did you redirect all pages with backlinks? You really should 301 everything. Did you change the links in the navigation? Are you getting any alerts in search console? Did the canonicals change? Did the category filters change? The simple answer is "find what changed". The complex answer is "find what changed". Do you have a copy of the old site? Run an audit on both. Sometimes you can also glean some insight from Google webmaster tools Pick up a copy of "ecommerce seo" by Traian Neacsu. He doesn't have an audit checklist per se, but anything you could be doing wrong is in the book.