Replacing shingles can be a little tricky. Among other things, the outside temperature has to be just right: warm enough so that the shingles already there can be pried up without damaging them and the new ones slid under but not so hot that the shingles are too floppy to work with. It is also true that doing it correctly means dealing with a larger area of the roof. I would not, however, accept a roofing cement patch as a finished job. It will not last long without leaking in addition to looking pretty sloppy.

Done right, the repair would mean patching the roof deck where the chimney came through (this might mean replacing a roofing board(s) or section of sheathing between rafters), adding a water barrier over the patch, then replacing the shingles. I would not accept anything less.

Hi Mainegrower,
Thanks for the info. I have read about the temperature difficulties with shingles. We live in Northern California,
so temperature should not be too much of an issue, we have many sunny cool days. I am not too concerned about the aesthetics, the hole is not huge. I am concerned about the leaking part. I think he did replace the roof deck and fix the sheathing, they replaced the ceiling and put in joists
in the room where the stove was. Is the problem that the tar is not a durable as the shingles for deflecting the water? Snow and hail are not really issues for us.

What did he patch the hole with? It would expect it to be sheet metal sealed with asphalt roofing cement.

The success of the patch depends on how many courses the hole spans. If it was wider than one course of shingles I would think it would be easier to add new shingles especially if the hole is near the ridge.

kiasu: If the contractor used fiberglass mesh to reinforce the roofing cement patch, it might (and it's a big "might")last a fairly long time. That kind of patch is still no substitute for the leak protection provided by overlapping shingles. I would imagine your roof is subjet to pretty wide temperature swings with hot sun and much cooler nights. The expansion and contraction of the roofing cement will sooner or later cause it to crack and allow water entry. The patch also very likely creates a low spot or uneven spot which prevents water from flowing off the roof as it's supposed to. All in all, the patch is an indication of substandard work.

"Is it really that big a deal to replace shingles"?

No, but it's more difficult if your shingles have been down for a good time and are sealed well. It's best to remove the shingles around the area early in the a.m. when it's cool and the shingles haven't had a chance to warm up. You have to be a little more careful as they are a bit more brittle when cold, but the seal tabs loosen easier when cold. A slightly curved flat bar with a nail pulling slot at the end works well to get nails or staples out from under the shingles that aren't being removed, but it's all about going slow and careful and making sure all fasteners that need to be removed are so that any left dont protrude through the existing shingles after the project is done. There are specialty tools to remove fasteners as well as nailing back under the existing shingles, but a flat bar and careful hammering gets it done as well. The shingles would be removed according to how they were layed out around the flume pipe hole removing full shingles. Cut out and replace the sheathing, lay down new underlayment,(ice and water sheild if close to the overhang and necessary in your area), re-waeve in the new shingles. Dont expect the new shingles to match up perfectly cosmetic wise. Often times even with the same manufacturer and color, they are off because of different lot numbers. Also make sure you get the same dimension shingle size wise as some are metric, while others are standard. They can differ width and length.