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Can I dissavow links on a 301'd website?
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 So we are performing link removal for a client on his old website (A), which is being 301 redirected to his new website (B). We have identified toxic links on site A and are removing, once complete we will undo the current 301, confirm a new GWT account for website A, and then submit the disavow report. We would then like to reapply the 301 redirect to site B while we are waiting for Google to process the disavow report, the logic being we can retain some current rankings on site B while waiting for the disavow to process on site A. Has anyone had experience with this method? I foresee some potential issues here but am interested to here from others on this. Thanks! 
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 I tend to agree with Federico's concerns. If the 301 transfers a penalty, the impact could be long-term, and it could be harder to rescue site B. The short-term ranking gains may not be worth it. Google hasn't been clear on how this operates with 301 redirects. John's suggestion to disavow on both sites seems safe. Worst case, it's wasted effort, but it's not much effort (once you've built one file, building two is easy). Still, you've got to wait for that to process, and if the algorithmic penalty is something like Penguin, then you'd have to wait for a data refresh. This could take months, so I'd be really hesitant to risk site B until you've cleaned up the mess. Once you disavow to site A, the 301-redirect should be fairly safe, but it does depend on the extent of the penalty. The risk/reward trade-off is definitely a "devil is in the details" sort of situation. 
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 Well, you are right, manual are easier to fix, although most likely, sites with manual penalties usually fall into an algorithmic penalty too. Steps I'd suggest: - Don't reinstate the redirect.
- Do some cleaning, extensive cleaning.
- Use it just as a redirection for users, but not for crawlers, rankings (using robots.txt disallow site A and 302 redirect the domain to site B).
 Hope that helps! 
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 No, this is an algorithmic penalty. Wish it was manual, would be easier to figure out. 
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 But did you get any MANUAL penalty on A or B? 
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 The problem is that despite the algorithmic penalty site A appears to be pushing heavy authority to site B and keeping decent rankings for some very competitive terms that we otherwise would not rank for with site B. If I remove the 301 I fully expect all current rankings to drop, I am trying to avoid this. Were doing link removal now, but plan on having to use the disavow tool once we have a few removal requests out to webmasters. I actually got an answer on this from John Mueller at Google in the technical SEO community on G+. John Mueller 
 "I would think about the final state you want to be in and just do that. If you want to do a domain move, then 301 and keep them. If you do a domain move + disavow links, then submit the file for both domains. This process will take quite some time (maybe even a year), so you don't want to play with it incrementally: just find out what you want in the end and set that up."
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 Hey Chris, Did site A or B receive a manual penalty? As any penalty on A, which is 301'd to B, will ultimately pass the penalty to B. I would suggest removing the 301 ASAP. Then cleanup the A domain until it's clean (if a manual action, until it's revoked) and then you can think of putting the 301 back. Removing a manual penalty could be a long process, it took 1 year for us and 4 reconsideration requests to get the penalty revoked. We had to use the disavow as a machete as disavowed almost our entire link profile leaving aside the domains that we knew were good links, all others were disavowed using the "Domain:" to avoid any missed link. 
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