Thanks! I hadn't thought about getting a second opinion but that sounds like a good idea.Sorry to hear about that (particularly because I have the same boat).
My 2 cents are:
1. It could be a serious problem. The stringers are like the studs in the wall supporting the house. If the stringer is rotted, the fiberglass bottom has no support structure behind it. A hard hit or increased flexing over time could weaken the fiberglass hull that could lead to cracks or a rupture.
2. I have not heard of this issue on our boats and don't remember seeing any other posts about rot in the stringer on this thread or the 400DA-410DA/400EC-410EC thread.
3. I can imagine that a repair of a stringer that runs past the engine room bulkhead into the cabin is not going to be cheap.
If it was me, I would want to get a 'second opinion' from a surveyor I know and trust and see what they find. I would not go to the boat yard/repair shop just yet until I confirm there is a problem.
Curious, does the paint on your stringer look in good shape? Any signs that water could be getting in anywhere? How does the stringer look in the area near the sump pump and by the bilge pump under the cabin entry stairs?