I believe it was Gawker or The Daily Mail that first published the Black Book in 2015. Nick Bryant author of the Franklin Scandal had a copy of the black book for years but he couldn't find an outlet interested in publishing the contents.

https://gawker.com/here-is-pedophile-billionaire-jeffrey-epsteins-little-b-1681383992

(The existence of the book has been previously reported by the Daily Mail. Gawker is publishing it in full here for the first time; we have redacted addresses, telephone numbers, email addresses, and the last names of individuals who may have been underage victims.)

The article claims that this is the full version but when you compare the contents we can see that there are pages left out and also the pages containing the handwritten notes.

But not before he had, according to the FBI affidavit laying out the crime, marked up the book and an accompanying notepad with "handwritten notes" that contained "information material to the underlying investigation that would have been extremely useful in investigating and prosecuting the case, including the names and contact information of material witnesses and additional victims."

When Rodriguez met with the FBI and handed over the black book he also handed over the notepad explaining that there were individuals how were not included in the black book which were implicated in crimes. The handwritten notes were add-ons made by Rodriguez.