Why the shingles are on the invoice
Asphalt shingles are nailed in overlapping courses, and once the sun has warmed them, a strip of sealant bonds each course to the one above it. Reaching a sheet of decking means breaking those bonds and pulling those nails across the whole area plus a margin, because rot reaches further under the surface than it shows from above. Shingles removed that way come off torn, creased or too brittle to lay again.
So the repair is a small re-roof sitting on top of a carpentry job. Beside the plywood at $675 to $975, the material list carries $420 to $672 of shingles, enough for about four squares with waste, a roll of felt, drip edge for an affected eave and roll flashing for any wall or vent inside the patch. New shingles will not match a weathered roof exactly, and the patch stays visible for a while. If you kept spare bundles from the last re-roof, hand them over.
Outside the price: rafters that have rotted along with the deck, ceiling and insulation damage inside, mold treatment in the attic, and whatever caused the rot. No permit is priced, since a patch this size is normally treated as a repair, but if the area keeps growing once the shingles are off, check with the building department before most of a slope is re-sheathed.
How rot gets found
From above, the usual first sign is a patch that feels soft or springy underfoot, often noticed by a roofer who was there for something else. From the ground you may see a dip between rafters, a course of shingles that no longer runs straight, or one area curling and shedding granules while the rest of the roof looks fine.
The attic tells you more. On a bright day with the attic light off, pinpoints of daylight through the deck mean wood has rotted through or pulled off its nails. Dark staining, white or fuzzy growth on the underside of the sheathing, plywood whose plies are separating and nails with rusted tips all point to moisture. Frost on the nail tips on a cold morning comes from moist indoor air, not from the roof, and it is the start of the same damage.
None of this measures the extent. The final count of sheets is set after the shingles are off, and it is usually higher than the first guess.
Find the cause, or pay for this twice
New plywood rots the same way as the old if the water keeps coming. Rot along the eaves usually points to ice dams or gutters overflowing behind the fascia. Rot in a ring around a chimney, skylight or sidewall usually means failed flashing, which should be replaced in the same visit. Rot spread across the upper part of the roof, with stained sheathing and no leak above it, is a ventilation problem.
Ventilation rot starts with warm, damp house air reaching a cold deck and condensing on it. A bathroom fan that empties into the attic is a common source, and so is an attic with exhaust vents but soffits packed with insulation. IRC section R806.2 sets the minimum at 1 square foot of net free vent area per 150 square feet of attic, reducible to 1 per 300 when its conditions are met. The roof ventilation calculator checks your numbers, and the roof vents guide explains how intake and exhaust have to pair up.
Patch now, or wait and fix the price per sheet
If the roof has years left and the rot is in one place, patch it now. Soft decking spreads, and a deck that sags holds water in the low spot. If the shingles are near the end anyway and nothing is leaking, it can make more sense to fix the cause and replace the deck when the whole roof comes off, because by then the stripping and re-shingling are already paid for.
Before signing for any re-roof, get a price per sheet of replaced decking written into the contract. Nobody can count rotten sheets until the old roof is off, and without an agreed rate that number gets set on the day, with your roof open. Ask the crew to mark or photograph each sheet before it comes out and to show the count on the invoice. A contract that includes a few sheets in the base price is fine, as long as the rate for any beyond them is written down too.
For a standalone repair quote, check the thickness. This estimate prices 23/32-inch CDX plywood, the heavy end of house sheathing, but the new sheets have to match the deck around them or the patch shows as a step under the shingles. A thinner existing deck means thinner sheets, which cost less.