It is a period of the timeline that doesn't have a lot of fluff for it at the moment as little was known about it before the Horus Heresy series of books began and the writers are still working their way up the siege of terra at the moment. Hopefully once Dan Abnett has written the epic that is the Emperor bitch-blasting Horus into a million soul fragments we will see a lot of writing about this period of the history.
According to Cypher many of the "foul traitor forces" were members of the nine loyalist legions, leftover Horus sympathizers and other Chaos marines who were rooted out with extreme prejudice. Granted, this is part of a "the reason you all suck" speech about the Dark Angels, telling them if they had just admitted to the Fallen existing during the Great Scouring they wouldn't be stuck being "the Unforgiven" so many thousands of years later. So take it with a grain of salt.