Use a scraper to scrape away the old caulk from the layers, or panels, of flashing between your chimney and roof. Dip a clean rag in acetate and wipe the panels thoroughly with the rag. The acetone should dissolve any remaining residue from the caulk.
Use a fresh damp rag to wipe off the panels. Dry the panels thoroughly with a fresh, dry rag.
Insert a tube of urethane caulk into a caulking gun. Remove the tip of the caulk tube with a scissors.
Position the tip or nozzle of the caulk tube so that it faces the roof edge of the flashing panel. Depress the caulking gun trigger slowly, and move the gun to run a bead of caulk across the edge of the chimney flashing where it comes into contact with the roof.
Repeat step 4 across all the flashing edges where the layers of flashing touch the chimney. Allow the caulk to dry.
Add a second layer of caulk to all the edges of the flashing over the first layer. Allow the second layer to dry.