Your chimney is perhaps the most vulnerable part of your roof. When you think about it, it kind of sticks out like a sore thumb. Perhaps the most vulnerable part of any chimney is the flashing around the base. This is the metal that surrounds the junction between the base of the chimney and where it meets the roofing. It is meant to keep water from settling in the corners around the chimney base and causing deterioration. Ultimately, if the flashing is not doing its job, you could end up with a leaky chimney flue and possibly have structural issues with your roof.
Get on the Roof
The first thing you need to do is get up on your roof and actually have a close look at the chimney and the flashing. Everything might look great from the ground, but it's hard to tell. Even if you don't have any issues with moisture inside your chimney flue, it is definitely worth repairing your flashing if it is coming loose.
Repair and Glue the Flashing
The problem with flashing is that it is usually glued onto a very rough tile material, whether it be stone, wood shingles, or asphalt roofing tiles. All of these materials have textures that make it difficult for even the strongest epoxy to hold the flashing down. Flashing is made out of super smooth aluminum that can also be difficult to get a good adhesive bond with. Since all of these components are exposed to rain and sun, they all react differently. Some materials expand and contract with the changes in temperature, making it very difficult for the adhesive to do it's job over time. Basically, the adhesive that secures your flashing is bound to peel away over time.
Instead of trying to just reapply the adhesive to the bottom side of the flashing, it might be easiest to just install completely new flashing. Using chisels and a utility knife, you should be able to pop the old flashing off. Some modern flashing products have adhesive backs that enable you to put them down like a sticker. You will still need to use heavy duty exterior caulk to seal the edges. Before you put your new adhesive down, you should check for water damage and clean off as much residue as possible. You want the surface to be clean so the new product will bond better with it.
With new flashing around your chimney, you are helping to protect the roof and the flue.