Twin Peaks Final Dossier. How much represents the new timeline? Almost none of it? Basically all of it?

Some of the discrepancies between the tv show and the Secret History of Twin Peaks, like Annie's story, were simply reconciled in the Final Dossier and shown not to be changes after all. But others are left unexplained, like Ben Horne surrendering in his Civil War delusion instead of winning as Robert E. Lee as in the show. Do remaining discrepancies like these simply reflect mistakes in remembering accounts (seems unlikely to get things that wrong), coded messages or intentional misdirection of some kind by the archivist or someone else, or timeline changes caused by Cooper's intervention? If the latter there must be some kind of rolling effect where some events are new and others original since The Secret History still talks about Laura's murder. If some of the Secret History already reflects the new timeline then presumably even more of the Final Dossier does since it was written later.