Whenever it’s practical to replace damaged roof flashing, do so. In an emergency or when replacement is too difficult or expensive, use a patch and inspect it annually. Typically, you can use this method for step flashing, which interlaces with shingles where they meet a wall or other vertical surface. However, it’s not practical to repair flashing at the valley where two roof planes intersect.
Insert new step flashing - Install new step flashing over the damaged step flashing (you'll likely need a ladder). Cut the flashing with tin snips, bend it in half at a 90-degree angle; slip the vertical half up under the siding or trim on the wall; slide it up the roof under the shingle and on top of or under the damaged piece. Adhere it using dabs of asphalt flashing cement under and over it.
Replace plumbing-vent flashing - Look for the leak. A plumbing vent can leak between the collar and the pipe, through the collar, or through the plastic or metal pan that fits under the course of shingles above the pipe and on top of the course below.
For leaks between the pipe and collar or through the collar, replace the collar or slip a repair collar over the pipe on top of the existing one.
For flashing leaks, install new vent flashing. Remove the shingles above the flashing, and install it according to the manufacturer's instructions, usually with finishing nails.
Repair chimney flashing - If the step flashing is corroded, insert step flashing as described in "Insert new step flashing," above. If the counter flashing is corroded, patch it until you can have it replaced professionally.
If the mortar joint where counter flashing is embedded is deteriorating, repoint the joint.
Patch open-valley or other exposed flashing - Clean the damaged area with steel wool.
Apply asphalt cement. In valleys, embed a flashing patch.