Never think in the terms of what's best for the search engines. Think of what is best for yourself to manage and what is best for your end visitors. If it is easier for you to do the previous on one website then do it. One thing to definitely consider is the history that these separate domains may have earned. The older the website/pages are the better they seem to do in the search engines. Also if these websites are doing well and getting traffic, why fix something that isn't broke?
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