A.Roofer Tom Brewer responds: Mixing up mortar is time-consuming and messy. Since the mortar can shrink as it cures, you don’t know how watertight the joint will be. Products installed with a caulk gun are much easier to install. When replacing chimney flashings, I usually use a polyurethane caulk. Silicone caulk and products like Quickcrete also adhere well to old masonry. Some people prefer products made for masonry, because they have texture. Whether you choose a product like Quickcrete or a caulk, using a caulk gun allows you to get the product into the tight spaces between the old masonry and new flashing, providing a solid, watertight seal and a clean, finished appearance.