Shemeska
Adventurer
Galeros said:1. Dragonlance's cosmology was separate before it became incorporated into the Great Wheel (around the time of Manual of the Planes). The Dragonlance Abyss and the Greyhawk Abyss weren't originally identical. MotP and 2nd edition AD&D even had to move Takhisis to the Nine Hells since she's lawful evil. So it's not so much a retcon as a retcon of a retcon, and we worked hard to clarify all of this in the recent DL gaming sourcebooks.
It wasn't so much seperate as it didn't have a cosmology before it was part of the Wheel. There was never any real suggestion of a seperate DL cosmology outside of some very vague notions in DL Adventures, which listed a few names of places but did not establish anything concrete. Later in 1e they were incorporated into the Great Wheel and those names were used in subsequent sources as names of divine domains as I recall, not much of a retcon if any retcon at all, the 3e DL retcon being more invasive on some levels, but the novels have always been vague enough to not really make one difference or another. It's debateable.
I could also just default to the notion of... Psst, the scholars on Krynn just didn't know what they were talking about, calling -every- evil outer plane 'the Abyss'.

2. Chemosh isn't chaotic evil, he's neutral evil. So either he's slumming in an Abyssal layer or he's not the Dragonlance Chemosh (who is incidentally a major player in recent Dragonlance novels.)
Chemosh is listed in the relevant 2e material (OHG, p180) as having his divine domain in the Abyss. The plane doesn't match his alignment, sure, but while most deities choose to carve out their home in a plane that does match them, it's not a strict requirement. Chemosh for whatever reason chose this route (perhaps to seperate himself from Takhisis in Baator?).