Should harmful links to your own website be removed?
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Upon running a link report on a website, there are often multiple links flagged as bad or suspect that come from a blog that is integrated into the website, which means there are links (set up as article tags) in the site that go to other pages in the same site. They have likely been flagged due to their high frequency. A similar problem is occurring where blogs from a connected site (from an offshoot site of a company that is part of the original) are also tagging their blog posts to link into the original website. Should these links be disavowed? Will these links have an effect on the website if they are disavowed or not?
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Is the blog on a separate domain or subdomain? Can you share the URLs?
Most likely you'll want to add rel="nofollow" to the links rather than disavow them, but it's hard to say definitively without understanding the site architecture as a whole and what you hope to accomplish. Regardless, you might want to dig deeper to find out why those links are being flagged.