‘Crack the cipher’ in this case most likely meaning: figure out the daily code word key you are using for that cipher.

If they have already gained the ability to decrypt today’s messages from station A in cipher A, and can therefore recover the plaintext of those messages; if they then find a message of the same length sent from station B in cipher B they can guess that that might be the same message, reverse engineer the key and maybe then decrypt all the messages being sent from station B in cipher B today.

Bletchley Park employed linguists alongside cryptographers, and the linguists would help permute the messages (substituting German words for common abbreviations, for example) to mount these sorts of attacks.