Given the rarity of this copy of the score, it is likely that most conductors have not seen Brahms’ original markings. Some of the markings written in his hand contradict those printed in the score. When listening to the London Symphony Orchestra perform this piece, it is noticeable that they do not follow Brahms’ pencil markings, but rather what is printed in the score. Is this because Valery Gergiev, the conductor, has never seen the score?
Shown here is Movement Two, pages 48-51 from the RBI score. There are Brahms’ markings in measures 273-274, and 288-290. In the first example, he marks in a decrescendo immediately followed by a crescendo to fortissimo. Next, he overrides a previous forte, marking it piano with a quick crescendo to forte one measure before rehearsal marking M. Listen to the recording linked below. You will hear that at this moment, the performers do not fall back to piano, but rather continue on at forte. There is a slight crescendo, but not as dramatic as Brahms had written.
Another place to ponder is measure 90-91 of Movement Four. Here, Brahms has written “ohne” (without) above the soprano line. This indicates that the soprano should not sing. However, it is rare that ensembles will remove parts like this in modern performances.