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Sorry I did not see your private message, but what happens is apple does not back up your jailbroken programs. So everytime you update your firmware you will lose your jailbroken programs.
You commented on my question (see below):
I used winpwn to unlock and jailbreak my iPhone 4gb running v 2.0. When the new release comes out (hopefully not long after the mac version today), how do I upgrade my software with the new version? Will I have to start from scratch and lose everything I did as well as the app store apps I downloaded or is there an easy way to do it? Thank you!
How would I go about backing up my iPhone up as you mentioned in your comment?