Non-combustible framing over existing timber frame

We are planning on raising the a portion of the roof of on our penthouse bulkhead, but seem to have hit a snag with the code rule for framing the structure. The original building (a factory from 1900) has timber framing. It is our understanding that new structures need to framed in non-combustible materials (ie, steel). However, we are also being told that we can't put non-combustible framing over combustible framing (the original timber framing). Obviously, we can't take out the original wood support columns from the building . So, I have no idea how to solve this for DOB. We've hired a structural engineer to come by, but any advice would be greatly appreciated.