During the Wars of Religion, as a member of the government of Henri III, Fauchet was forced to flee Paris in 1589 and could not return until 18 April 1594, now in the service of the new king, Henri IV. During this absence, Fauchet's Paris residence was sacked, resulting in the loss of his library: more than two thousand volumes, by his own account, many of which were manuscripts. Many medieval manuscripts once belonging to Fauchet now reside in the Bibliothèque nationale de France and the Bibllioteca Apostolica Vaticana in the Vatican, while some are scattered across Europe's libraries (Bibliothèque Sainte-Geneviève, Paris; the British Library; Berlin State Library; Dijon Public Library; National Library of Sweden; Burgerbibliothek of Berne; Biblioteca Ambrosiana) and still many others remain unaccounted for.