It is well known and frequently lamented that the Archive of the Holy Office in Rome is inaccessible even to serious scholars. Behind this obstruction of legitimate research there is nothing more sinister than bureaucratic obstinacy and inertia, which time may overcome. Actually, if the doors of the Congregation for the Doctrine of Faith (formerly the Inquisition) were to be thrown open tomorrow we probably would not find terrible secrets; in fact, we would find relatively few documents, mainly doctrinal decrees and the paper of the now defunct Congregation of the Index, which were transferred to the palace of the Inquisition when it discontinued its censorship activities in 1917.
The Archive of the Holy Office was impoverished by several terrible depredations. The first occurred on 18 August 1559, when a Roman mob celebrated the death of Pope Paul IV by sacking the headquarters of his most cherished institution, liberating its prisoners and burning its records. A second took place more than two and a half centuries later when, to fulfill Napoleon’s dream of a central archive for the empire and a supra-national center of learning in Paris, valuable books and manuscripts were removed from libraries and archives of conquered Europe, including the Vatican. More than three thousand crates were distributed over several convoys; the first set out from Rome in the dead of winter, February 1810, and attempted the long and laborious journey over the Alps. The convoys were accompanied by archivists of the Church, whose feelings we can imagine when they watched two wagons disappear into the rushing water of a torrent at Borgo San Donnino, near Parma, or when eight cases slid into a canal on the road between Turin and Susa.
John Tedeschi, The Prosecution of Heresy (1991)