Cut the damaged section of the existing seal with a utility knife to remove it. Use a putty knife for leverage if you need to pry or peel the sealant from the window frame.
Apply a caulk remover to especially difficult or aged sealants in keeping with manufacturer's instructions. Allow it to dissolve the broken seal for the time printed on the product label.
Clean around the double-pane window frame with a damp rag and wipe away any visible residue. The exposed seams cannot be contaminated with anything that could possibly trap air beneath the seal.
Cut the nozzle on a tube of silicone caulk with a pair of scissors; leave an opening in the tip one-quarter inch wide or less. Insert a stiff wire into the opening to puncture the seal inside.
Load the tube into the caulking gun and dispense a bead of silicone into a joint where the window frame meets the wall. Draw the tip of the tube along the space to evenly fill the seam where you've removed the old sealant.
Quickly glide a wooden craft stick over the silicone application for a neater seal before it takes on a tacky texture. Allow the new seal to cure overnight, or over a full 24-hour period.