What is the effect of a proxy server replicating a sight on SEO
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I have heard of PPC company's that set up a proxy server to replicate your site so that they can use their own tracking methods for their reports. What affect if any does this have on SEO for a site?
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If the server was not publicly reachable (i.e. just on their intranet), then there would be no issues.
If the server was accessible to the public, then as long as the site was blocked with a robots.txt file search engines would not index it. There would be no reason for anyone to link to the site, so it should be invisible to search engines. At least Google/Bing will respect those settings, and they are all that really matter.
I would be most comfortable with the above but if you want to be extra cautious you can set up a canonical for each page back to the main site. You would need a script to either add or modify the canonical tag on every page.