Inspect the installed plumbing vent pipe boot's rubber for cracking or splitting, either of which requires that you replace the old boot with a new one. Pull out the nails from the boot using a hammer and remove it from the roof.
Insert the new vent pipe boot's flashing under the shingles that sit above the vent pipe, prying loose any roofing nails holding the bottom of the shingles down using a pry bar. Place the other side of the boot's flashing on top of the roof shingles.
Make pilot holes where the nail holes in the vent pipe boot's flashing sit on the roof, drilling through the shingles and into the wood below. Drive screws through the holes in the flashing and into the roof using the guide holes.