What to do about real backlinks spiraling out of control and affecting domain trust flow
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I have a site with a few hundred thousand backlinks and many of these are are legitimate, but the source site of the backlink often has a low authority and is broken, causing a spiral of bad backlinks from pagination, comment replies, etc. For example one site may have 4 legitimate backlinks with a spiral of 400+ bad backlinks, this is happening across dozens of domains.
My site is more authoritative than these broken backlinks and regularly receives highly authoritative backlinks, because of this would it be best to disavow these spiraling low authority domains, attempt to contact the webmaster and add a nofollow, or any other solution?
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I think you've answered your own question.
If it was me and those "spiraling backlinks" were affecting my domain trust flow, I'd do just as you suggest and attempt to contact the webmaster to come up with a solution. They may not realize the harm they're doing and be happy to learn how to improve upon their own site. Try to negotiate a win-win so they're more likely to conform to your wishes.
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If the site has low authority and hundreds of backlinks, it's probably a spam site. You're wasting your time to reach the webmaster to get the links removed. They are not linking to you to help you, but to help themselves by association with a high authority site.