Old chimneys on slate roofs can be problematic when the flashing has worn out and the chimney is no longer in use. The solution is to remove the chimney top and “erase” the chimney from the roof.
1) Set up a safe scaffolding system around the chimney using hook ladders, ladder jacks and planks. You may also need some roof jacks. Remove the chimney top down to the roof.
2) Tear out the old flashing and remove all broken, partial, or tarred slates. Take the chimney down below the roof. Lay a slate over the hole as a cover. You may have to scab some 2x4s on the rafters at this point to allow for nailing the replacement roofing boards.
3) Nail or screw roof boards into place to cover the hole. Use the same type of lumber that the roof is made of (in most cases, 1 inch boards). The boards must be the same thickness as the existing roof decking.
4) Install the replacement slates. Try to use the same type, size, shape and age as the existing slates and reuse the existing slates as much as possible. Sources of salvaged roofing slates.
5) Finish the slating, first one side, then the other. Finally, install a new ridge section. The chimney removal work should be almost invisible when done. This same procedure can be used to remove most roof penetrations on a slate roof.