If I was you, I would contact the embassy and ask them, what exact documents are required, also I would register your 3rd child's birth with the embassy in Brunei, if you have not done that already. also I would contact the DFA in Philippines, I am sure some would be able to sort this out...

I remember when we were getting our daughter passport in the DFA, we had a few problem,with her NSO birth certificates which took a few weeks to sort out...

will