Sometimes books just get lost, or simply thrown away when they have exceded their usefulness, to put it bluntly. By the time Queen Isabel died in 1504, the knowledge on the Indies had advanced quite notably, as you can see from maps like Juan de la Cosa's, the anonymous map purchased by Cantino, or the famous Kunstmann maps that show Alonso Vélez de Mendoza's expedition. By 1504, Columbus' own words on the first navigation had been made obsolete by the expeditions organized under the purview of bishop Juan Rodríguez de Fonseca, who had taken over the whole American enterprise after Columbus was stripped of his titles and honours.

Things were different, of course, in 1493. When Columbus made it to Barcelona in mid-April of that year, the information he had was basically exclusive and of paramount importance, hence why the Queen felt the need to have a copy of Columbus' diary of the first navigation, which took quite some time to make, as the Queen explains in a letter dated the 5th of September 1493, which I quote:

Don Cristóbal Colón, our Admiral of the Ocean Sea, Viceroy, and Governor of the islands and firm land recently discovered in the Indies, with this courier I send you a copy of the book you left here, for it has taken quite long as it had to be made secretly so that those from Portugal that are here would not know of it [...]

Had Portugal known in full detail what Columbus had seen and anotated, they may have never renegotiated the treaty of Alcaçovas. Furthermore, Portugal had even tried to stop Columbus' second expedition, an idea that abandoned their heads once the Fleet of Biscay showed up to escort Columbus' journey. At that point, that one manuscript was of the most extreme important for the state, and its contents would be a state secret.

By 1504, it did not matter that much anymore. The book does not seem to appear in any of the inventories of books owned by Queen Isabel by 1503, let alone those inventories made after her death. These inventories are readily available thanks to the transcription made by Diego Clemencín in the 19th century, digitised here (pages 430 to 471)So, it can be further said that not only was the book lost by 1504, but even by 1503.

Christopher Columbus, though, received a copy of his own writings in September 1493, just about when he was ready to set sail on his second journey (which he did on September the 25th). This copy must have been kept in the family's archive, managed by the admiral's bastard son Ferdinand, a great bibliophile who had a truly massive library by the time of his death.

Bartolomé de las Casas worked on a copy he commissioned from that copy, and he notes errors from the copyist every now and then. Even worse, the version we know from Bartolomé de las Casas is rather abridged, but we can trust its faithfulness by comparing its text with the version present in Ferdinand Columbus' "History of the Admiral". Link to Las Casas' manuscript here

What exactly happened to the copy made in 1493 and sent to Columbus later that same year? We may not know for sure. With the passage of time, the Biblioteca Colombina suffered all sorts of problems, from lawsuits on the posession of the books, ranging to natural disasters such as floods, passing through plain old theft and pillage caused by wars. The diary that belonged to Columbus simply disappeared from records. Just to give you a figure on the scale of the tragedy, of the 17,000 books owned by Ferdinand Columbus, fewer than 2,500 are preserved.