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Mike said it all. What could affect your SEO in a way, although only very slightly: Reciprocal links from both domains to the other domain. As they both reside on the same webspace, which is obviously on the same server, that has the very same IP-adress for both servers... they both sit on the same Class-C IP-network. Links from domains that reside on the same Class-C tend to not have the same impact as links from other Class-C networks. But as your linkbuilding shouldn't rely too much on two links you won't run into massive trouble here.

The index.html file name offers no value for SEO nor users. I recommend not using it and directing users to a "clean" URL (eg seomoz.org/ instead of seomoz.org/index.html). As long as you properly set this up and consistently link to the same URL there are not any duplicate content issues. If you wish to go one step further you can add the canonical tag to your page.

Although it isn't the best - Yahoo Site Explorer is pretty "fresh" and should show them pretty quickly.