After the entire event, will I be able to regain access to the island when the machine goes back there or is this a permanent thing where pirates can't get in?

1-1/2 hours ago, Keith said the Ocean Depths vending machine is now located in Delphi Beach...read the news.

And yes, once the event is over, you'll be able to go to the Islands, assuming of course you've turned in the Uncharted Lands Map.