Yesterday (6/8/2017) fmr FBI Director Comey testified that President Trump told him during a dinner which the 2 of them had (with no witnesses present) something along the lines of "I hope you can let the investigation of Flynn go". This was after Flynn was already fired for lying to the VP about the extent of his conversation with the RF embassador. Comey testified that he believed the POTUS was making a request to drop the investigation about whether Flynn had lied on his release forms about that conversation.
Dershowitz (a life-long Democrat and a very credible Constitutional scholar) has said that a President is fully authorized to direct the FBI to conduct or to drop an investigation. In fact, that's the reason the special prosecutor's office exists. A President cannot order the special prosecutor to drop any line of inquiry. But as the chief executive officer of the executive branch, he can simply direct FBI not to spend any resources on an investigation of someone who he believed was already punished "enough".
My question: could Comey avoid the whole situation by simply asking the President "is that an order?" Comey testified that he was stunned. But, presumably, he did come out of his stupor at some point and he did have a chance to consult with the lawyers. And since he knew the expressed wishes of his boss, could he not ask the same question formally at a later time? He testified that he chose to continue the investigation without clarifying with the President whether this was the President's expressed opinion or a request. But why would he not try to make it clear (even at a later date) by asking?
It has been suggested by some on this site that a President can even go so far as to refuse to prioritize fighting a war declared by Congress if he so chose (because he has the prerogative of setting executive priorities). In the same vein, it would seem that he certainly has the power to shift investigative priorities and even order a case to be closed unless it's outside of his chain of command (again -- special prosecutor). What would be the legal status of the investigation if Comey did ask "is that an order" and POTUS answered "yes"? What would be the legal status of the investigation if he answered "no"? Is there any reason (legal reason) why Comey would not pose such a question (even at a later time)?