The Thraddash will survive the Ilwrath onslought if you are allied with them. So now you can rest easy knowing your Thraddash students will be relatively safe under your watchful eye. However, just like any war, there will be losses. Your students will incur a 25% reduction in battle strength that is reflected on their Sphere of Influence.
You must also keep in mind that the one thing the Thraddash absolutely can not tolerate is dishonesty. If you steal their Aqua Helix during the Ilwrath conflict your students will turn on you. All of the ships you built at the shipyard will defect back to the Thraddash fleet and your former students will incur a 100% loss in the battle against the Ilwrath.