The flashing should be installed under the top and side shingles but it should be laid above the shingles that are below the vent pipe.
How to replace vent flashing on roof.
There s no need to lace the flashing pan into the shingles since the boot and bell of the new flashing will shed water around the damaged part of the old one.
Leave the bottom of flashing exposed so only the sides and top are covered by shingles.
Pull the old flashing up over the vent pipe and scrape any old caulk and debris off the roof.
If there is a split in the shingle along the edge of the flashing be sure to caulk the edge of the flashing.
The neck of the flashing should fit snugly around the pipe.
How to install step flashing with a wall corner.
In simplest terms a new vent pipe boot flashing is slid over the top of the existing one and the top edge of the pan is lapped beneath the overlying shingle course.
To replace flashing around the vent pipe first remove the shingles covering the flange at the back and sides.
Pry and lift off the flashing.
Hammer the nails into the top and sides of the flashing.
Bend the corner flashing tightly around the corner.
Nail it in.
Replace the shingles and cover the nail heads with roofing cement.
Ensure it sits flat and extends at least 8 inches above the shingles.
Pull or cut off any nails.
To make the installation easier you can turn the flashing as you lower it in place.
Slide the new flashing over the vent pipe and under the shingles above the pipe.
Slip a flat bar under the edge of the vent flashing and pop the nails up photo 1.
Cut your shingles precisely to leave at least half an inch around the base.
Take a second piece of flashing and set it down in place.