1 What will happen to the airplane vis-a-vis the larger aircraft?
2 So long as the cargo bays are open will the airplane continue to fly normally?
3 Will it start to lose its balance for lack of air under or over the wings?
4 What will happen when the cargo bays are closed completely?
5 What will happen if the cargo bays are closed but the larger aircraft has a mechanism that preserves and mimics the airflow before it swallowed the airplane?
1. As the larger aircraft with its open cargo bay (really a bomb bay) approaches from above, nothing at all will happen until the larger plane either moves down, or the smaller plane moves up - and the forward bulkhead in the larger plane actually blocks airflow across the wing of the smaller airplane. This will happen with increasing turbulence, linearly, and once completely blocked, the smaller plan will begin to fall with acceleration due to gravity at that rate. If the larger plane is quick, and if it begins a slow dive when the process is attempted, it may close its bomb bay and capture the smaller plane.
2. When the bomb bay begins to interrupt the flow of air the smaller plane will experience turbulence, then will cease to generate lift, and will appear to fall as if you fired a ball straight out from a tennis machine - in an arc towards the ground as its thrust still exists but its lift is gone.
3. Yes. As air doesn't move in straight lines at flight speed when encountering surfaces - it is quite likely to experience severe turbulence.
4. airspeeds being similar and loss of momentum due to turbulence discounted - the smaller plane will need to immediately idle its motors. If this doesn't occur, than since the airspeeds are essentially equal and now that the only limiting factor to your airspeed (drag) is gone - your smaller plane will rocket forward at the rate prescribed by its motors. In the bomb bay the smaller plane effectively starts at 0. Now if you kill the motors and survive this risky maneuver - the plane settles gently inside the larger plane.
a. If you are the only vehicle aboard the Amtrak "Autotrain" - say you have a Geo. And also pretend that the autotrain is a single car - hundreds of feet long just to give you enough room. When the Autotrain is at 70mph traveling from Florida to DC, and your Geo is idle in the back of the car, your Geo is traveling 70mph. It gained this energy from the locomotives engines. Now if you start your Geo and floor it - in the 200 feet or so of train that you can traverse - if you also get to indicated 70mph, your Geo is now effectively traveling at 140mph.
Now since an airplane motor doesn't use it's wheels to propel itself, it either uses a propeller, which sucks in air and blows it back behind it, or a jet engine, which uses combustion to generate thrust that is fired behind it (and of course airflow other than engine inlet air doesn't matter), with the motors on the acceleration it experiences as it moves forward as it lands inside the motor is a function of drag and weight vs thrust.
5 would make things easier for the pilots involved as the turbulence factor would be reduced. It would be more complicated to get the smaller plane to stop as you would need to reduce motor output vs airflow generated through this magical mechanism.