Did you see the drawing shown with the article?
The cottage and wings are clearly built in stone block, and these can be numbered and reassembled as they were inside and out.
Any infill will just be exactly that, and not relevant to the appearance or shape of the structure.
They're not suggesting the work will number things at the pebble level - this work only applies to the built structure, the stones the masons would have prepared.
Be interesting to know if they planned on retaining the wood. Fine if it is preserved, but if various forms of rot set in over the years, they might have to open an account at the nearest B&Q
I think it means exactly what it says - after all, they would hardly try and fit the same mortar or lime back in place... they'd mix new.
Now you've also got me wondering if there is any original decoration to be taken down and refitted later.