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Thank you Paul. Lessons learned: Do track both www and non-www sites separately as you suggested. I noticed on the Google Webmaster Tool, it even recommends tracking https if the site moves to the secure environment from http. I do see the results being slightly different, but not a lot. The big difference in the results I noted earlier (site crawl issues) was because the scanning was still in progress. After a couple of days, the numbers got much closer together.