After reading your thread, I see that you are sensitive to other feelings . inpsectors, contractor, and engineers. This is all supposed to be normal thing and it happens all the time. Is your contractor the General contractor or are you? The general contractor is the one who works out the ruffled feathers. When I was flipping a couple rooms as general contractor, I had issues with city, city inspector, what contractor wanted to do, and other inspectors for various utilities. Its just a matter of listening what THEY perceive as the right way of doing things and personally suggest things to see if it matches everyone satisfaction. 9 times out of 10 I was able to resolve things on the spot but half f the time it may not be what i wanted to do, but it shuts everyone up.
Since the work has been stopped, the contractor was right to step away till its resolved because a stop order is harder to deal with then paperwork being resolved. But in your case, you need to get an personal attorney, not a lawyer to resolve the paperwork between the new inspector and city and have your engineer firm CC'd into it.