You can install step flashing after installing shingles only if you remove surrounding shingles to properly integrate the flashing, as step flashing must be interwoven with shingle courses to be watertight, not simply placed on top. Step flashing is designed to be installed in layers where each L-shaped piece is placed under a shingle course and over the shingle course below, creating a stair-step pattern that directs water down the roof. If you attempt to install step flashing over already installed shingles without removing them, water will run behind the flashing and cause leaks. To install step flashing after shingles are installed, you need to carefully remove shingles along the wall or chimney area using a flat pry bar to break sealant bonds and remove nails, exposing the deck and wall. Then install new step flashing starting at the bottom, placing each piece so it overlaps the previous piece by at least 2 inches and is nailed to the deck, not the wall, allowing for movement. Then reinstall shingles over each piece of step flashing, ensuring each shingle course covers the flashing except for the exposed lower edge. For chimney flashing, you also need to install counter flashing cut into mortar joints over the step flashing. While possible as a repair, it is labor intensive and risks damaging surrounding shingles, especially if they are older and brittle, so professional installation is recommended.
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