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I have all the bad links, they are all 404's now.

Thanks Travis but there are no crawl issues

Alright...weird...the search results show some https but when I click on them I get the "SSL Connection Error"

I don't have that version of the site...If I try to go to https://website I get an "SSL connection error"

I have a client who has definitely been penalized, rankings dropped for all keywords and hundreds of malicious backlinks when checked with WebMeUp....However, when I run the backlink portfolio on Moz, or any other tool, they don't appear anyone, and all the links are dead when I click on the actual URL. That being said, I can't disavow links that don't exist, and they don't show up in Webmaster Tools, but I KNOW this site has been penalized. Also- I noticed this today (attached). Any suggestions? I've never come across this issue before.

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Having a second page with duplicate content can hurt your rankings. I would re-direct

We recently re-designed our company website, and the knowledge graph no longer displays when Googling our company name. I've searched for info on this, and even spoke with someone from Google, and it seems like there are no real answers. Our G+ profile is optimized and we're even a part of the Google Partner network. I've had the site re-crawled, and everything is okay in webmaster tools. Any insights? Thanks.