I'm sure Saurik has a huge queue of signature requests that may take awhile to process. He has to be careful with how often he makes requests to Apple's servers or he might get his server IP's banned.
Once 3.1 is jailbroken and you need to restore, you will edit the /etc/hosts file on the computer that is running iTunes and set the IP address of the Apple authentication servers to Saurik's IP address. Then when iTunes goes out to get the signatures for your device ID, Saurik's servers return the stored version.
The details are posted on Saurik's site:
http://www.saurik.com/id/12