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I have two separate domains set up on one hosting account through godaddy.  Will this affect the SEO negatively?  They are completely different sites with their own unique domains but on my local files the second domain is set up as a subfolder for the original hosted domain.  Any thoughts?  Thanks in advance.

Should I redirect index.html to "/" or vice versa?  Which is better for duplicate content issues?

In the link analysis of my site, it's not showing inbound links that I know we have?  Why is that?  I have verified they are still existent.