The Air Accidents Investigation Branch said specialist contractors joined the operation in “challenging conditions”.
It was carried out in “as dignified a way as possible” and the men’s families were kept updated throughout, it said.
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The wreckage of the plane, which vanished two weeks ago over the English Channel, had been found off Guernsey.
The Piper Malibu N264DB was en route from France to Cardiff, after the 28-year-old Argentine striker’s made a quick trip back to his former club Nantes two days after his £15m transfer to Cardiff was announced.
Mr Ibbotson, 59, from Crowle, North Lincolnshire, was at the controls when the flight lost contact with air traffic controllers on 21 January.
An official search was called off on 24 January after Guernsey’s harbour master said the chances of survival were “extremely remote”.
However, the wreckage was located thanks to a privately funded operation, led by marine scientist and oceanographer David Mearns, who then called in the Air Accidents Investigation Branch when he found the wreckage.
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