The FAA for the sake of their international credibility are going to want to know why they were not told of the issues that have been recently publicly disclosed and will need to be seen to be taking corrective action.
As to the long term future of Boeing, whilst the current regime will do its best to protect the company by the time the cases come to court the political landscape may have changed The continuing failures of other programmes such as the frankentanker are not going to help the company in Washington.