As 15159 says, there's a conversation between Ahriman and his mortal 'apprentice', the empath who's name I forget. Lem...something. The chapter had always been called the Thousand Sons, in fact I believe it was suggested that it was one of the only chapters never to be renamed when the Primarch took over.
When the mutations took over, and Magnus made his deals to save the rest, there were only 1000 left. At this point in the book, Lem* says 'so why were they called the Thousand Sons before that, if you didn't know how many would survive'?
Ahriman has no answer.