Actually, if the original flashing was cracked, then sliding new flashing down on top of it like these pictures would generally fix the water intrusion in most cases, possibly getting years more life for the cost of the $5 boot. Toss in a little silicone between the boots and Bob's your uncle. You could even cut the flats off the 2nd boot, and just slide the bell down with caulk... if you don't like the happy-go-lucky appearance