I think that the flowchart for actions in general, for a heavily automated aircraft (which I'm sure your project would be) would not change a lot in the case of pilot incapacitation. You'll be adding the common sense actions required to get the aircraft to the quickest suitable landing site for mediacal assistance, but not while causing increased risk to the flight.
We fall back to the basic prime directive of safe flight, in its order of importance: Aviate - Navigate - Communicate. Do only as much as you can, assuring that aviating is always being done first. If half your crew resource is lost, a few things may be delayed, while the remaining crew member flies safely. The rest will fall in place. If an accident happens in the mean time, it was going to happen anyway. It will be less severe than if control of the aircraft was lost. Once you squawk 7700, you probably just took care of navigate and communicate all in one.
So, stepping aside from the "checklists" for a moment, I'd be concentrating on the aircraft design, if there is an option to embody provisions to minimize the impact of such an event.
If the tiltrotor is in any phase of flight where thrust is being directed anywhere other than directly horizontal, an accidental control input of any consequence is probably unrecoverable, but design the provision in to minimize the impact if you can.
If the aircraft is fly by wire, the design opportunity exists to allow one pilot to take control away from the other. Obviously, for the sake of crew harmony, this would be used only for emergency, but it's worth having. Two ways of accomplishing this: Big red "I've got it" button (but that requires an additional action), or more subtly, defining a "normal" control motion range, and an "emergency" motion range. Whoever moves their control into the emergency range last, has total control of the aircraft. So, if pilot A falls over the stick, and pushes it full travel, pilot B's instinctive reaction wil be to apply a whole lot of input to his stick to correct the situation. Pilot A's stick never got emergency authority, as it got in the range first. A's stick maintians control until B's stick goes into emergency range, then the computer realizes that A's input was for the wrong reasons, and B's is trying to return to controlled flight. This could be linked to the computer's knowledge of the aircraft attitude. B has total control until things change favourably.
The other thing my wish list would have built in, would be an "other" pilot controlled motor on the inertial reel of the shoulder harness, so it could be used at a suitable speed to winch an incapacitated pilot upright in the seat, harmlessly away from all the cockpit knobs. Car seatbelt "pre-tensioners" do this in harmony with airbags to some degree, but for different reasons.
Other than that, if the incapacitated pilot is not interfering with the safe operation of the aircraft, the flying pilot should be expected to continue to fly the aircraft safely (or he really should not be there). If the systems are so complex that he is having trouble coping with the workload, just give him more time. As I said, 7700 goes a long way in this regard, and if someone on board is incapaticitated, it just became a "medivac" flight, which has the highest priority in flight.
Back in the 80's I was a very inexperienced right seat pilot in a Piper Cheyenne, when the pilot suddenly took ill. Although he maintained conciousness, and was not in dire circumstances, he withdrew from flying for the remainder of the flight. I took my time, used the normal checklists, and there was no problem. Yes, if something had quit, the tension would have ramped up quickly, but we do what we can. This is not a safely threatening event, if pilots are well trained.