Honestly I don't think this would be a really big problem.
But to be absolutely sure nothing bad can ever happen(TM):
Why not have purpose built catching planes match up with them, once they are low and slow enough? I imagine something Airbus A380 sized, or large Antonovs, C5 Galaxy, releasing a clamp or hook on a cable or boom, connecting to that glider in the air. And tow it to its designated splash down area.
Like in https://en.wikipedia.org/wiki/Mid-air_retrieval
There! Solved that for you :)