It is possible that the reason Andross constructed Herbert, or at least the reson he loved him so much, was because Andross was raised by foster parent android pigs.
Herbert mysteriously appears again in chapter 5, in Andross's possession once more. It turns out (perhaps a retcon) that the android pig stolen was not Herbert. Nonetheless, it was full of top-secret data regarding Venom, allowing Peppy Hare and Slippy Toad to sneak into Andross's control chamber and destroy Herbert. Without power, Andross's telekinetic aplifier became vulnerable allowing Fox McCloud to destroy the power core.
It is later revealed that after its destruction, Herbert's remains were kept in the rebel base on Papetoon.
While Andross was restoring his powers on Fortuna, he was seen with Herbert II. He also set out with Andross's speeder and Monarch Dodora. But when the Star Fox Team turned the creature against Andross, Herbert II was seen weeping above his debris.
Herbert II then went to the ruins of Venom and following Andross's instructions in a pre-recorded message, he was responsible for his cloning using strands of the Ape's hair, and a psycho-print of his brain patterns.
When Andross's clones attacked Papetoon, Herbert joined the in the assault. It's not clear which was which, as Slippy realised that original Herbert's remains mysteriously vanished, presumably to join his master's forces. After his armada was destroyed, Herbert accompanied Andross's Dancing Insector, and then followed him to the Black Hole.
Andross's association with pigs in the comics may have been carried over into the games since Pigma Dengar has been a frequent associate of Andross.