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We had a similar problem we thought with duplicates after placing canonical tags on all our pages. Moz took about a week as did Woorank to update and decide the canonicals were in place and showing no duplicate content.

We have a fairly small site with a little under 100 pages but this was a significant amount of work inserting the canonical tags and we were a little worried initially that they continued to show as duplicates for a short time.

Gary

We just went through this exact same change for marketing reasons. With a combination of 301 redirects and a ton of new content we found our organic dropped significantly on day one but after a period of about two weeks now things have bounced back and in some cases the new content has allowed us to rank better.

Our previous site had tons of outdated code and was not particularly clean. Pages now load much faster, the new look seems to have increased the number of pages per visit as well as time on site. If we had to do it over again tomorrow we certainly would. Sometimes not renovating the site I think costs you more in the long run.

Hope this helps.

Gary