BnF fr.15919 includes letters (1567-1569) of Scipion de Fiesque (Scipione Fiesco), who was sent to the court of the Emperor Maximilian II for the marriage of King Charles IX with his daughter (before the marriage with the younger daughter was finalized by Albert de Gondi (Wikipedia)). (Catherine de Medicis' letters to him in the volume are printed in Lettres de Catherine de Médicis (Google).)
Many letters to the Queen Mother and two to the King (f.100, f.158) are partially in cipher. The reconstructed key below will allow reading undeciphered portions.
While some ordinary letters are used in the table, plain letters are often used as nulls, particularly at the end of the line (but not limited thereto) (e.g., f.79, f.94). On f.39, "Jay par moy [symbol]" just before the ciphertext is struck out, but these are words and symbol that are used as nulls elsewhere.
Cinq Cents de Colbert 398 includes many letters from Jean de Vulcob (1575-1576) (p.33,p.257,p.284,p.311,p.321) and Guillaume Ancel (1576-1578, 1584) (p.365,p.439,p.443,p.449,p.467,p.501,p.513,p.525,p.539,[p.561,p.565,p.569,]p.599,p.621), resident ambassadors to the Emperor Maximilian II.
The reconstructed key below will allow reading undeciphered letters.
The nomenclature entries are represented with letter groups.
Vulcob's letter to the Queen Mother dated 2 August 1572 (BnF fr.18989) also uses this cipher.
Papers related to Poland in BnF fr.15967 include undeciphered letters to Henry of Valois in June 1574. Henry had been elected King of Poland in 1573 and had been in Poland for a few months when Charles IX, his elder brother, died in May 1574. He secretly left the castle on 18 June and, via Bohemia, Vienna, and Venice (Martha Walker Freer (1888) Henry III, King of France and Poland: his court and times, Vol.1, Chapter IV (Internet Archive)), returned to France, to be crowned King Henry III in February 1575.
The letters in question are written just about this time: f.167 (8 June 1574) and f.180 (22 June 1574).
The cipher can be solved with the help of CTTS: CrypTool Transcriber & Solver developed by George Lasry and the CrypTool team. The key is as follows:
The letters, regarding John, Voivode of Modavia, who rebelled against the Ottomans (Wikipedia), are from someone who talked with a Pasha. As it turned out, the cipher is the same as the one used between François de Noailles, Bishop of Acqs, French ambassador in Constantinople and the Duke of Anjou which I reconstructed from BnF fr.16142 (another article)!
The deciphered copies of these letters appear to be extant and are printed on p.522-523n and p.523-524n in Négociations de la France dans le Levant, vol.3 (Google).