After viewing the Miniseries quite a few times I can say there were some scenes deleted. Recall if you will an article, an interview with the intoxicating Raelee Hill were she mentions a long scene between her and Sikozu and Scorpius. http://www.farscapeworld.com/news/shownews.php?id=169
Also, remeber the second trailer? My personal favorite snipit of the trailer was Scorpius walking away, inside what looked to be the command carrier, saying, "I shall show you how to win a war." During the same trailer there was a shot of Chiana pointing what looked like to knives at Scorpius on Moya, right around the time the annoucer says enemies thrown together for a war nobody wants. Any others we may be aware of? I hope the DVD has the scens, where the Original Trilliogy -Star Wars DVDs did not have deleted scenes.
Scorpius: And you have ruined something unique.
Scorpius: I... do not loose!