The best way for a do it yourselfer to repair a roof boot is to seal the existing boot and apply a new rain and repair pipe collar.
Replacing roof pipes collars.
Figuring that the rubber collar on the new flashing may split before it s time to strip and replace the roof shingles another 20 years hopefully i first seal the vent pipe to the metal of existing flashing with protectowrap s form flash 2 flashing tape.
The collar and sleeve looks like the new construction version without the roof flange slides over the plumbing vent pipe and damaged boot flashing.
They also make a boot flashing repair version.
This old house general contractor tom silva shows how to create a watertight seal around a vent pipe.
These collars provide a permanent seal that just about anyone can install.
The bell shaped base encloses around the dome of the original boot flashing and sheds water around it.
However replacing the entire flashing can be quite involved and may require the application of new shingles.
You can also replace the entire flashing around the pipe.
See below for a shopping list and tools subscribe to.
Vent pipe collar skirt for vent pipe care and maintenance.