Is $5,000 to replace the front half of the roof due to a soft spot a fair price?

I recently discovered a soft spot on my roof, which I estimate to be roughly 30 sq ft. I was hoping a patch job would be possible, but the roofing company suggested more extensive work. I'm unsure if replacing an entire side of the roof for a small bad section is standard practice and am considering a second opinion. We recently purchased the home, and the roof appears relatively new, but I'm unaware of any warranty. I understand insurance might not cover it since it wasn't caused by a specific event. I'm concerned the soft spot could lead to an active leak and further damage, as I feel the rest of the roof still has a lot of life left. I'm not sure how old the roof is, but it visually seems pretty new. The wood under the soft spot is stained from water, but I don't think it's actively rotting yet. A chimney inspector noted questionable flashing around the chimney and felt the wood was wet under the roof, which might be the cause.