A lightning bolt does not separate air...it is not a phisical thing! The thunder is caused when lots of air is ionised and heated to a very high temp in a fraction of a second. The heat causes the air to expand violently=>thunder.
The sonic boom on an airplane can only be heard when the shockwave created when breaking the sound barrier reaches the ground. Again this has nothing to do with air "returning". It is just a violent pressure wave.