If you look in the comments the poster mentions that the original versions were done in Lightwave and Aftereffects. It has been leaked that one of the companies,Digital Muse, the artists all kept their own copies of the files (http://trekcore.com/blog/2013/05/deep-space-nine-in-high-definition-one-step-closer/), and that they had purposefully over built them (besides HD, I guess they were also thinking at that time that if a future theatrical film needed one of the ships, by overbuilding, the ships would be ready for theatrical resolution). Plus the CGI model of both DS9 and Voyager are still in use for the Ships Of The Line calendars (actually, it was the CGI artists on Voyager who launched the idea for the calendars, because of all the work and detail that they had put into the Utopia Planetia yards for the opening of the Voyager episode Realativity, and how they hated the fact that people were only going to see blurry, low resolution shots of the orbital facility).
Just to add that the approach they were taking back then also meant overbuilding for things like close ups and pull back shots from Windows etc. Was the final shot of DS9 full cgi or mixed?