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The 301 redirects were still in place at the timeDoes this mean they are not in place any more?
I have since reset the change of address request in WMTNot sure what you mean there - you withdrew the Change of Address or you have done Change of Address again?
google-site-verification: googleXXXXXXXXXXXXXXXXXXXXX.html
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>404 Not Found</title>
</head><body>
<h1>Not Found</h1>
<p>The requested URL /googleXXXXXXXXXXXXXX.html was not found on this server.</p>
<p>Additionally, a 404 Not Found
error was encountered while trying to use an ErrorDocument to handle the request.</p>
<hr>
<address>Apache/2.2.3 Server at <website> Port 80</address>
</body></html>
That above was actually written to the verification file. This was not in the file originally and do not know how the verification file has changed. Could this possibly be the cause?
As far as you know, was the verification file present continuously? I suspect that a lot of people automatically delete it after google's first visit (I know I did once), thinking it only gets checked once-and-for-all.
RewriteEngine On
RewriteCond %{HTTP_HOST} ^site.com
RewriteRule (.*) http://www.site2.com/$1 [R=301,L]
RewriteCond %{HTTP_HOST} ^www\.site\.com$
RewriteRule (.*) http://www.site2.com/$1 [R=301,L]
I have changed this today (it was sitewide) and will post any results.
OLD WEBSITE ---301---> NEW WEBSITE ---Canonical---> OLD WEBSITE
As a matter of interest, have you only removed the Old Site canonical or have you replaced it with a correct New Site URL?
Please do report back your results, but do not forget that it may take Google some time to re-crawl all the pages from the New Site.
To see if you are on the right track, you may want to try to do WMT "Fetch as Googlebot" and then "Submit to Index" of a few selected pages with fixed canonical and monitor these to give you the indication on whether it would work.