how did the kahana find the island?

So the purple sky in the season 2 finale, with the hatch being destroyed, along with the electromagnetic energy, this caused the communications to be destroyed. As a result anyone who left the island, could never come back. So Ben had to get surgery on the island, rather than go to the main land. the submarine was destroyed about day 82. This means when Tom met Michael to get on the freighter, he saw him no less than two weeks from when he left the island. since the communciations were down at the same time Michael left, how did Tom get back on the island to be killed by Sawyer???