Basically, the timeline works until March 2006, when Roger dies. From then on it gets rather patchy. The first story to really break the timeline was The Pickens County Horrow which made references to the time being 2012. Throughout Abe Sapien Dark and Terrible and B.P.R.D. Hell on Earth this has gotten worse. The stories are for the most part treated as if they are set in the same time period that they come out, but the time that elapses between each story is relatively short, creating an ever widening gulf between when the story is set and when the story should be set according to the timeframes mentioned by the characters.
I've basically given up at this point. The timeline's a mess. All I really care about is when an event happens relative to another event. So the current Abe Sapien story is set after The Devil's Wings, but before End of Days.