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Backlinks showing for wrong site in Webmaster after 301 redirect mess

I had an issue with changing an IP address for a site during a 301 redirect process that caused backlinks to be credited to the wrong site in webmaster tool. The IP issue is fixed buy I’m wondering how long it will take google to see everything is fixed and for webmaster tools to credit the backlinks correctly.

Here is what happened.

I run my sites on a dedicated server. I did a 301 redirect from website A to website B. The sites were identical and this was for a domain name change only. This website needs a dedicated IP for SSL. Since they both needed a dedicated IP during the redirect, website B was given a new dedicated IP. Everything went fine with the 301 redirect. Website B took over the search rankings for website A without a drop in search ranking or traffic.

A couple of weeks later, I redirected website C to website D. Again, they are identical and this was for a domain name change only. This site also needs a dedicated IP for SSL. Since my server has a limited number of IPs, I put website A back to the server shared IP. I used the dedicated IP for website D that was previously with website A. The 301 from site C to D went through but there was a moderate search ranking and traffic drop.

After a couple of weeks the old backlinks from website A showed up in webmaster tools for Website D instead of for Website B. It was then that I realized that the server was still routing website A traffic to it’s original the IP address that now has website D on it. Everything in WHM on the server looked correct. The tech at the web hosting company wasn’t sure why this was happening either. We re-pushed the DNS data to propogate again and this fixed the problem.

Now everything is fixed and the old backlink from website A correctly get routed to website B. Here are the issues. I think that website D took a ranking hit because of all of the new backlinks for completely unrelated content, The websites are not even closely related. I’m also a little concerned that when the 1500 or so backlinks get correctly routed back to website B that it will look like 1500 “new” links since they didn’t transfer correctly during the 301 redirect process that was over a month ago. I’m not sure if this will appear “spammy”.

What a mess! Has anyone experience something like this and have an idea if the SEO will work itself out now that it is fixed? I’m hoping website D will recover the rankings and traffic that website C had. I don’t want to disavow 1500+ links. I think this would be a red flag. I would prefer if it just worked itself out naturally now that the technical issue is fixed. I’m just not sure about how it will shake out.

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