If Colonel Vessery attacks one section of a Huge ship, and that ship has a red TL token on the section he is not attacking, can he still gain his own TL through his pilot ability? I suppose this hinges on whether the entire ship is considered 'defending' or just the attacked section, since the card text says "...you may acquire a target lock on the defender if it already has a red target lock token."

From the Huge Ship rules:

Target Lock Tokens

A ship that acquires a target lock on a huge ship must acquire that lock on a single section of the huge ship. The closest point of the chosen section must be within range. The red target lock token is placed next to the chosen section of the huge ship and its effect only applies to that section.

So, one could assume that for Col Vessery to work, he would specifically have to attack the section with a red target lock token on it.

Yeah, that's how I ruled it too. But it got me curious, and I wanted to make sure for future references.