Dark Tide: Siege by Michael Stackpole was going to be the second book in the Dark Tide Trilogy. Set in 25 ABY, it was to have detailed the New Republic planning for the next Yuuzhan Vong attacks following, with Corran Horn dealing with Shedao Shai's threats. A ship that would have appeared in Siege was used on the cover of Dark Tide II: Ruin.
When Siege was cut, the trilogy became the Dark Tide Duology, with Siege's major plot points being merged into the other two books. The extra book allowed LFL to stretch James Luceno's Agents of Chaos from one to two books.