What if I point my canonicals to a URL version that is not used in internal links
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My web developer has pointed the "good" URLs that I use in my internal link structure (top-nav/footer) to another duplicate version of my pages. Now the URLs that receive all the canonical link value are not the ones I use on my website. is this a problem and why???
In theory the implementation is good because both have equal content. But does it harm my link equity if it directs to a URL which is not included in my internal link architecture.
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Quite honestly, I would never use a canonical to point to a page that no-one can navigate to. If I were Google, I would look at this and wonder if it was a recommended page, why then was this not the one people can just click on.
Andy
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Hi Andy,
I agree, it does not seem like a logical solution. Do you know of any documentation on this, maybe even from Google? I would like to give some guidelines to my web developer based on a source.
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Allright, maybe a good question for the Google Webmaster Help Forum right?
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I don't know of anything that will explicitly tell you not to do this, but you can find lots of general information here:
http://support.google.com/webmasters/bin/answer.py?hl=en&answer=139394
Andy
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It certainly can't hurt. You might get someone pointing you to documentation relating to this exact problem

Andy
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I think Andy's absolutely right - I've seen too many situations where mixed signals caused crawl/index and even ranking problems. Ultimately, the canonical URL should be canonical in practice and used consistently. Otherwise the canonical tag is just a band-aid.
The other problem is that you naturally end up attracting links to your non-canonical URLs, because those are what people can see. Long-term, that compounds the situation.
Now, is it catastrophic? Unfortunately, that's really tough to say. I've seen situations where Google honored the canonical tag even without internal links and the site was ok. I just think it's a significant, unnecessary risk. Unfortunately, like Andy, I don't know of any clear documentation on the subject.
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Thanks again. I hope Google will come out with some real guidelines on this subject. It  saves us time arguing with third parties.
For now I will get the canonicals fixed.