Below are ciphers in the correspondence of François, Duke of Guise (1556) collected in BnF fr.20974, "Clefs de la correspondance chiffree de Francois, duc DE GUISE, avec quelques lettres de lui. (1556)" (Gallica). (Only the substitution alphabet and nulls are shown. For the nomenclature etc., see the original. The numbering is mine.)
These ciphers mainly employ arbitrary symbols, except for no.6, which mainly use Arabic figures. Some of the other ciphers (e.g., no.15) also use figures.
There are some undeciphered ciphertexts (see below).
no.1 (p.1-4) undeciphered ciphertext (see below)
no.2 (p.5-8) Cipher between Guise and "le general Dalbeyne" (16[?] January 1556)
no.3 (p.9-12) Cipher between Guise and le comte de La Mirandole
no.4 (p.13-16, 17-20) Cipher between Guise and Dominique Du Gabre, eveque de Lodeve (Wikipedia)
no.5 (p.21-22) Cipher between Guise and Anne d'Este, duchesse de Guise (Wikipedia)
no.6 (p.23-24) Cipher between Guise and M. Marie de Sainte-Fiole
no.7 (p.25-28) Undeciphered ciphertext (see below)
no.8 (p.29-32) Two undeciphered ciphertexts (endorsement on p.30 "Monsr de Lyvet"?; subscription on p.32 "A Monsr ..."? illegible). I solved this cipher to find the key as follows. One characteristics of this cipher is an accent-like sign in the symbols for "a" and "m". A codebreaker may be led to a wrong hypothesis that this sign is an apostrophe or an accent in the plaintext.
no.9 (p.33-36) Cipher between Guise and Raymond de Fourquevaux (Wikipedia) (A cipher between Henry II and Fourquevaux is in another article.)
no.10 (p.37-40) Another Cipher between Guise and Dominique Du Gabre, eveque de Lodeve
no.11 (p.41-44) Cipher between Guise and le cardinal Charles de Guise (Wikipedia)
no.12 (p.45-48) Cipher between Guise and le cardinal Francois de Tournon (Wikipedia)
no.13 (p.49-52) Cipher between Guise and "les ministres du Roy a Romme"
no.14 (p.53-56) Cipher between Guise and Hercule II d'Este, duc de Ferrare (Wikipedia)
no.15 (p.57-60, 69-72) Cipher between Guise and Hippolyte le jeune d'Este, cardinal de Ferrare (Wikipedia)
no.16 (p.61-64) Cipher between Guise and le cardinal Simonelli
no.17 (p.65-68) Cipher in Italian "Zifra col ... Duca di Guisa"
no.18 (p.73-76) Cipher between Guise and le capitaine Nicolas Franciot de Lucques
no.19 (p.77-80) Cipher between Guise and Blaise de Montluc (Wikipedia) (1556)
no.20 (p.81-84) Cipher between Guise and le marechal Charles de Brissac (Wikipedia)
no.21 (p.85-88) Cipher between Guise and Renee de France, duchesse de Ferrare (Wikipedia) (1556)
no.22 (p.89-92) Another Cipher between Guise and Hercule II d'Este, duc de Ferrare
no.23 (p.93-96) Another Cipher between Guise and Blaise de Montluc "dont lon se sert a Romme"
no.24 (p.97-100, 101-102, 103-104) Cipher (endorsement on p.100 illegible; p.104 "pour Monseigneur O[?]")
no.25 (p.105, 109-112) Cipher between Guise and "M. de Boulain"
no.26 (p.113) Cipher
no.27 (p.115) letter to "Madame ma maistresse"
(p.116) endorsement "... Chiffre"? illegible
no.28 (p.117-120) Cipher "pour Madame"
no.29 (p.121-124) Cipher
no.30 (p.125-128) Cipher
no.31 (p.129-132) Another Cipher between Guise and le marechal Charles de Brissac (Wikipedia)
There are undeciphered ciphertexts in BnF fr.20974. The images below show their beginning.
The strokes in the second specimen seem to indicate word boundaries.
The following is my transcription of the first five lines:
There are some distinctive patterns, which allow some hypotheses (as below) but I have not been able to find a viable clue.
The two ciphertexts on p.29-32 are easy ones. The cipher is essentially a simple monoalphabetic substitution cipher (see above), and the ciphertext retains spacing between words.
While the first pattern I tried (like "oisk88iA") did not find a plausible match, the second pattern I tried (like "sf2s2βif") gave a match "proposer." From the findings "i"=e and "s"=p, I thought the first pattern would be "depasse*" or "depanne*" (which eventually turned out to be "deputtez" or "deputtes"), partly because I thought "oi" and "ois" would be "de"/"des" or "le"/"les" from their occurrence on their own. Then, "der**eres" must be "dernieres" or "derrieres", of which "dernieres" was consistent with other occurrences. Then, it was clear that "i*s*r***ions" was "instructions."
The beginning of the two messages reads something like below (* is an unidentified symbol, possibly a null):