Charles letter for Para son.
Toddler Chandler Biddiss, three, is blind and severely disabled. His 34-year-old dad Paul, from 3 Para, was refused home leave for his birth.
Paul claims his absence led Chandler to get meningitis when mum Debbie couldn't look after him and their four other kids.
Now, as Colonel-in-Chief of the Parachute Regiment, Charles has risked a clash with MoD chiefs by writing with his support.
Charles wrote: "You have a very brave son who, I hope and pray, will overcome these appalling obstacles."
St James's Palace said: "The letter is a private correspondence."
Kosovo veteran Corporal Biddiss, from Oxford, has been fighting the MoD for three years.