They are still with the imperium?
Chaos ships are the warships of the great crusade, light cruisers are mostly used as scouts or escorts for convoys.
Also, Chaos has plenty of excommunicate forgeworlds they can use to reconstruct the skartix engine.
Well, first, the great crusade would have needed light cruisers even more then IN does today. Remember that the Great Crusade was not called The Great Walkover. It was the Imperium against thousands of, in some cases equally well equipped, human stellar empires. Second to support a war of conquest on a galactic scale would require vast amounts of supply, the convoy's transporting said supplies would be vulnerable.
Horus' fleet is stated to include light cruisers in the HH books in a few places.
No, you mistake the fluff of the Slaughter. The Dutiful destroyed the forgeworld where the Scartix Coil design was kept. It doesn't mean there was only no other Slaughters built unlike the Acheron's fluff where it says only one as far as records show. A lot of AM also turned renegade during the Heresy and Chaos has their own forgeworlds in and around the Eye of Terror. More recent fluff however implies that more Acheron's were built in the Eye of Terror. Aside from which the Planet Killer was built in the Eye. Parts also aren't that much of a problem when you have supernatural forces aiding you in the ship's operation.
If by flattening a single forgeworld they destroyed the Imperium's ability to produce these, then this would indicate that only this forgeworld produced Slaughters. Using the dates given and the rate of production of the Murder class hull as a yardstick, you have a maximum of 20 of them or so having been built, assuming that that Forgeworld did nothing but produce Slaughters the entire time.
As far as using the warp as an excuse: why not simply build 1,000 ships for every one that the Imperium has and just win? It would be about as easy, since the warp is an ocean of infinite power.
Also, Chaos has plenty of excommunicate forgeworlds they can use to reconstruct the skartix engine.
The problem with that is that we have an approx amount of time that has passed, from the perception of the Chaos legions. While ten thousand years have elapsed in real space, in the eye of terror, it's only been about two centuries according to fluff, from the point of view of the CSMs. Further, given the nature of Chaos, it's not terribly likely that, even if they had a break through, the fallen forgeworlds would share data.
