As I understand it, because the visa is void and was never activated I should still be able to apply for another one although its difficult to obtain a definitive answer.
The reason for the transit visa was because i didn't want to start the clock on the 12 month working holiday visa for simply passing through the country for several hours and leaving for over month.
At the time I was unaware this would void the working holiday visa previously granted.
As you say it may be best to seek the advice of an agent.