What novels have been proven wrong? The only thing wrong with the novels are the game adaptations, and that's because the books are written for the most part before the game movies were made, even before the cast was hired, bringing some inconsistances to small details. The books also expand on the story, giving the stories more realism by putting the characters in broader experiences, instead of having every single chapter a fighter battle.
Anyways, don't think that the entire fleet was destroyed at Kilrah. Granted, it was huge, but the Kilrathi were building up a fleet for years well behind the front lines. The same fleet we see destroyed is the same fleet we see destroy Earth on the loosing streak of the game. That does not mean it was the entire fleet, there were still fleets in defensive and offensive action all across the galaxy. It was commented that the Kilrathi would still win the war even though their home planet was destroyed with all the power they have, that comment was countered with the fact that the destruction of their home would be a great moral loss. The destruction of the fleet probably evened the odds between the Confederacy and Empire. If not for the surrender, the war would have waged on for years to come.
Although the major warships were scrapped at the end of the war, individual clans and warlords kept their ships. Although they weren't a direct threat to the Confederation, there were numerous border conflicts following the surrender.