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I am not too sure about it. I've seen one project in the past where a site most likely was penalized after the same kind of scenario and it was much less pages that were indexed. The site didn't rank for over a year for it's own domain name.

Also I am not sure about the thousands of indexed pages, if I can just let them become 404 errors or if I should do some redirect. Or perhaps should I remove the pages from the index via WMT?

I am currently considering buying a Website because I would like to use the domain name to build my project on. Currently that domain is in use and that site has a few thousand pages indexed and around 30 Root domains linking to it (mostly to the home page). The topic of the site is not related to what I am planing to use it for.

If there is no other way, I can live with losing the link juice that the site is getting at the moment, however, I want to prevent Google from thinking that I am trying to use the power for another, non related topic and therefore run the risk of getting penalized. Are there any Google guidelines or best practices for such a case?