i am a little confused with this, children did not have their own passports I don;t think, and travelled on the passport of their parent , guardian or institution.
If he sailed, aged 2, did he not travel with the family?
Did you actually look in the passport and read that he left the UK?
Have you checked passenger lists, including Bernardo lists, for the surname?
From the birth certificate, are his parents the same as your father's? If so, was your father born after the family returned to the UK? Or was your father born in malta?
Was your granbfather serving in the armed forces when the family left the UK? If so his regiment and number should be on the boy's birth certificate.
the records for the regiments based in malta in the 1920s will be with the Chaplins records, probably now at the National Archives at Kew.