Apple released the beta for iOS 4.1 earlier today and there have been some rumors that Apple may display a watermark on the phone that it is jailbroken, just like Windows shows a “Not Genuine” alert for PCs.
Also, iOS 4.1 has new encryption technology, that will constantly check if iPhone or iPod touch, have been jailbroken. This is done by digital watermark that appears when iOS is jailbroken, and this watermark cannot be removed, even if reverted to unjailbroken status. Apple store employees will check for the watermark during iPhone service.
However, @MuscleNerd from Dev Team has said that just like earlier rumors about the AT&T OTA jailbreak detector, this “Watermark” encryption is just rumor. This comes from a guy who has been working on jailbreaking the iPhone for quite sometime now.
So rest assured, the Watermark encryption should be not be a problem, and even if it does you can be rest assured that the Dev team will take care of it.