PDR, the FAA (and EASA) routinely issue "Special Conditions" and Issue Papers during the development of a new aircraft. Special Conditions are typically used when new technology isn't adequately covered by the existing regulations. For example, when FADEC was first introduced, there were no meaningful regulations regarding Electromagnetic Interference (EMI), so there were special conditions for HIRF/Lightning resistance (it took another 20 years before the FAA actually finalized regulations for HIRF - so all the Boeing FADEC and FBW installations prior to the 787 were covered by Special Conditions. Issue papers are used similarly when meeting the letter of the regulation may not be 'adequate' and to make sure that the method of compliance used is acceptable. There is also the ever popular "Equivalent Safety Finding" - where the design may not meet the letter of the regulation but meets the safety intent of the regulation (Boeing thrust reverser installations post-Lauda have all used an EFS - the FAR says the aircraft must be controllable - that's not practical (maybe not even possible with big high bypass engines) so Boeing has instead designed the system so an in-flight deployment won't happen. Granting an ESF requires an Issue Paper on the subject.
This is all long standing SOP (due to all its advanced technology, the 787 had a huge number of Special Conditions, Issue Papers, and ESF). Boeing would be negotiating with the FAA and EASA on the requirements long before it formally launched any blended wing/body aircraft.
IMHO, if we see a blended wing aircraft, the first one(s) will be for the military - likely some sort of cargo aircraft.