I too often wondered why these immensely important papers were "cut" in this way. Some authors suggested it was because some passages the Queen thought unsuitable for preservation, e.g Christopher Hibbert says the following:-
"In fulfillment of a charge imposed upon her by her mother, Princess Beatrice transcribed passages from the journals and burned the originals when she had finished with them. She often went further than this, destroying whole entries which she thought unsuitable for transcription and substantially altering numerous passages which she did transcribe.."
It goes on to say that on the instructions of Edward VII, the letters of Queen Victoria to Lord Granville were destroyed, as well as some to Disraeli. (The ones to Disraeli were "about various members of her family")
(quot. fr."Victoria: a Personal History" - Hibbert.)
I think it was a "daughterly duty" why she did it, and though i've always felt it to be such a literary loss, one can understand she felt bound in honour to the promise she had made to her mother..