Old masonry chimneys
Nearly every older house in this region has one, and it is the most complicated thing on the roof: a masonry stack passing straight through the covering, weatherproofed by a set of metal pieces that have to move with both the roof and the chimney without ever letting go.
Three details that all have to work
Step flashing runs up the sides, woven into the shingle courses. Counter- flashing sits above it, and this is the piece that matters most here: it is supposed to be cut into a mortar joint and folded down over the step flashing, so water cannot get behind it. And the crown — the concrete cap on top — sheds water away from the masonry. On a century-old chimney, all three have usually been repaired at least once, and often in the fastest way available.
The shortcut to recognize is surface caulking: counter-flashing sealed to the face of the brick instead of cut into the joint. It looks fine for a few years, then the freeze-thaw cycle opens the seam and the water goes straight down the outside of the chimney and into the framing. On old mortar it is not merely a shortcut — it is a repair that cannot last.
On a replacement
Reusing chimney flashing is the most common reason a brand-new roof leaks in its first year. Ask whether the step and counter-flashing are being replaced, and whether the counter-flashing will be cut into the mortar. If the masonry itself needs repointing, that is a mason’s job rather than a roofer’s, and it is far cheaper to do while the staging is already up than to schedule separately six months later.