You have touched on a very sensitive subject that not many are prevy to.
I doubt anybody can give you answers in a public domain where the answers to you questions are Confidential & Priviliged.
The Corps of Engineers have their own software that cannot be used by anybody unless they are screened through the FBI and CIA and approved to use the software.
There are structural engineering companies that developed their own proprietary software to be used by their own employees that are approved for accessibility to sensitive information.
This reference could be a good start on the topic, also refer to FEMA 427