Have an assistant hold a ladder securely while you climb onto the roof.
Pry up the shingles and removing nails, if necessary, covering the base of the boot. Be careful not to crack or tear the shingles. Locate any nails in the base of the boot and pry them out with a flat pry bar. Cut the silicon sealant around the edges of the boot with a utility knife.
Slide the boot up and off the roof penetration. Clean the penetration and the roof under the base of the boot with a brush. Slide the new boot onto the roof penetration. Hold up the shingles around the boot while settling the boot into position.
Install roofing nails along the top edge of the boot and part of the way down the sides of the base. Install the nails in locations that the shingles will cover.
Run a bead of silicone caulk around the edges of the boot base. Lay the shingles back onto the base and press them flat. Install roofing nails in the shingles if you removed any while changing the boot.
Run a bead of caulk around the top of the boot, where the penetration protrudes through the boot.
Climb back down the ladder, while an assistant holds it securely.