The British High Commission in India is incorrect.
It's sufficient that your son qualifies as a
Returning resident (
18). A passport with the ILR was just one way of showing that he qualifies. Lost of passport doesn't make him any less qualified. However, showing that he qualifies may be more difficult. Do you have the UBKA's letter confirming his ILR status?
Moreover, possession of an Entry clearance is also not mandatory (
2(a)) in this
category. Unfortunately, your son is a
visa national. That's the reason for asking a CIO to authorize travel, so that the airline will not be
afraid of being subject to any fines. Hence, he may bypass applying at the British High Commission.
Have you yourself tried to contact a CIO at the airport terminal where you son will be travelling to?
Perhaps
UKBAbble can help you more?