The letter to Judge Kimba Wood stated that “the Government was advised that the FBI’s original electronic extraction of data from telephones did not capture content related to encrypted messaging applications, such as WhatsApp and Signal… The FBI has now obtained this material.”
This change is likely because of the way the messages are stored by the applications, not because the FBI had to break any sort of encryption on them. WhatsApp and Signal store their messages in encrypted databases on the device, so an initial dump of the phone would have only provided a cryptographic blob. The key is required to decrypt the contents of such a database, and there are tools readily available to access the WhatsApp database on a PC.
In a post to Twitter, attorney Michael Avenatti, who represents Stormy Daniels in her suit against Cohen over a nondisclosure agreement regarding her alleged sexual encounters with Donald Trump, crowed about the new evidence.