The first step is cleaning the islands - transfer any creature and all the important ressources to a ship and then destroy all buildings. Make sure the ship are some miles away from the coast line...
There´s a new island.json: http://cdn.atlasdedicated.com/islands.json to be placed in the data-directory. After that, the faulty islands are not available any more and you can replace them with other islands of the same type - I´ve used same sizes to avoid changeing discovery zones.
Existing buildings will be stuck somewhere in the ground or the air so it´s important to clean the islands first.
Do the same as above - there are four different freeports left in the new json with the ending "_E"
I replaced all island via texteditor (copy&paste) and apart from some bugs with some ressource everything looks quite OK and I really hope I don´t need to wipe.
Doing it with the grideditor only might work as well, but be sure to have a copy of your servergrid.json! Changeing the number of islands might result in database-errors and then the server has to be wiped.
A complete map should have 9 Powerstone-Islands (_PVE), 9 Unterwater-Trenches, a grid for the Kraken and the ice-cave-island. It´s a hell of work doing this from the scratch.
I´ve used the 3*3 Mythic Seas-Map and modified it