one option would be wipe all physical items from the map but leave player levels and exploration as is. for the players that have taken the time to sail and explore this would be the hardest hit as it takes weeks to sail the map.
if they wiped all structures and land claims that might be enough. another way to do it is announce the wipe a week or more in advance and have the freeports as safe zones. you can load up a ship with tames and go to the freeport before the wipe and your ship in the freeport would be safe. Hell make a great race out of it too. once the servers come up