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If you are using a 301 from an old site to a new site, that is where the problems appear to be happening. I do not think PageRank has any relevance in this instance, at least based on my experiences. There are also many topics here and at other fora where the above has been confirmed.
We did the same thing on the 13 September and things haven't resolved themselves as yet. Our PR is now back where it was (in the 1st Jan update) but our traffic is around 50% of previous levels.
The lesson from google would appear to be: never take down an existing domain, just leave the site up and create new content for the new site.
I have been trying to move my site from "site.com" to "www.site.com" using 301's for a year and no success. :-(
The homepage shows as www.site.com but the rest of the site is without.
My last attempt: delete everything old using Google's " automatic URL removal system." and leave only the home page. Bite the bullet as I wait for G to index the site from scratch.
Since Google never seems to get which pages must go and which are duplicates I thought it needed a litle help.
I will post the results... if ever.
My reasoning is that one of my sites has dropped considerably in the rankings.
About 7 months ago I used a 301 redirect on 4 old sites to a main site after it had previously been hosting the identical content on four different domains.
For 3 months this worked and the main site enjoyed good rankings, that is, until the latest update.
After the site dropped on this latest algo update I performed a site search on the main site and the old domain is now appearing in the main sites results! So I performed another site search on the old site and it has 21 pages cached from may last year. There are links pointing to the old domain and this seems a likely reason why google is refusing to give it up (as it has now recognised that the 3 other old domains are not in use now)
So the way I see it, there are two options -
Or try the google remove url tool on the old domain?
Has anyone used this tool before, any warnings, advice etc..
I will post the results here
It works, but once you remove it, it's removed. You can't "change your mind" a month later.
Suposedly is a temporary remove (90 days). Unless you put a robots.txt in your root to specifically prevent the pages from being re-indexed.
Check Google's explanation here:
If you remove the whole site, well, that could be another story.
In my case I have the homepage indexed properly so I am deleting the rest and keeping the 301 redirects in hopes that Google will re-crawl the site under www.domain.com/ as it should.