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I can see cases for using the .edu domain. If you are in the business of educating people at your facility, at their facility, or on a website  then I would definitely start using the .edu domain. If you are a publisher of academic content that is really good content and recommended by professors and used by students then I would use the .edu domain. There are many domains that clearly communicate the business of the organization.   They bring "credibility even if undeserved"... and if you really deserve it then the .edu domain could be like throwing gasoline onto a fire in terms of attracting natural links and pulling clicks in the SERPs. Which domain would you click (or type in) if you were looking for an educational organization named "wilson"?   Which one would you be more inclined to link to? Wilson.com or Wilson.edu There are .edu domains being used by organizations that are in the business of education, but most of their activities would be considered to be something other than students and teaching.  Smithsonian.edu, Getty.edu, GIA.edu. Have you ever sent a link request to a website suggesting that they link to the most valuable page in the internet for a topic and they write back.... Wow!  That's a fantastic article, but we don't link to commercial websites? If you have a website on wilson.com and send a link recommendation to loc.gov or nasa.gov, what are your chances of getting a link?   Does that change if your website is on wilson.edu?

I totally agree that is scary, but then again safe. But if I were in your shoes, I would make the change over a period of some time. As you are actually making the changes, which am guessing takes some time, you can at the same time uploading them so that Google views this effort as it is, an effort, and not a one day thing. but on the other hand, you are not doing something wrong, just remember not to over-optimise!

You may want to see the latest google webmaster hangout . John Mueller answers a question about this type of topic. You may also want to see the seo journal article linked to this. John Mueller has also stated a number of times that there is no duplicate penalty as such but my interpretation of that is that you wont rank as well as the original source. Many affiliate sites suffer from this kind of thing as they are share the same product descriptions etc. Pete