The supernova occurs during the third of four scheduled convoys before the Vega node collapse.
Petrarch says the evacuation must be "completed" before the Vega node is collapsed, but just because Command decided to stop evacuating people doesn't necessarily mean there were no more people to evacuate. It's entirely possible that Command just gave up, figuring the risk of keeping the node open would be too great. It's also entirely possible that some people refused to leave, figuring that the Shivans weren't interested in destroying planets this time around. Naturally, they wouldn't have reckoned on the supernova...