My take on changing timelines, mainly based on the FD, is that although things happen in a different manner, the same end results occur; hence, Leiland still kills himself, Coop still comes to Twin Peaks, and Ronnette is still attacked in the railroad car and escapes. With Laura now disappeared, 'Time' still has to find a way for the attack to happen. Maybe Leo and Jacques use the railroad car in this timeline instead of the cabin for their private 'activities.' 

Doesn't explain the discrepancy of Ronnette seeing Laura disappear into the woods in the FD, though.

Unless the book is an indication of a 3rd alternate timeline...

Those little differences can add up to a lot of change,    though.      Just look at Laura for one,   there is a huge difference between someone simply vanishing,   or finding an obviously murdered person.