Ruth I have already suggested that your husband gets in touch with the embassy here in Manila or Hong Kong where passports are now processed
explains the situation and asks them for requirements and costs then between you it can be dealt with
Dont worry the Brit system isnt as convoluted as the Philipine one for these kind of issues
The difference is that a Passport app is not the same as a visa app where you pay granted or not and as your son is British by descent he has right of entry to the UK and The EEC