The iPhone's entire filesystem is Flash based. Whenever you browse a web page in Mobile Safari the iPhone writes to a cache in Flash. Whenever you receive an email, the iPhone saves the message in Flash. Whenever you synch a new song, it is written to Flash.Hardware is as sensitive to being re-flashed a lot as it is to being dropped on the floor,
Jailbreaking may cause the iPhone to misbehave because of improper programming techniques used by one of the unauthorized programs you install. It has nothing to do with the simple act of reflashing.
The warranty on jailbroken iPhones is void because the software license agreement was violated. Whether or not the service technicians are able to detect the fact that the software license agreement was violated in any given case is another story.