Ok to make a new quick mission region open on of the .rgn files in your scenario folder in notepad. You will see something like this:
Code:
VERSION 3
BEGINREGION Australia_Northern.rgn <Name of Map
LATLONG -12.044881 138.339935 <Location of map
Alter those values and save the file under a new name. and you have a new quick mission region.
Now there is a problem with that, the areas that ships are generated will be like in the old map, so if the terrain is too different you may end up with ships starting on land. That has something to do with the other lines of code in the file. I have not messed with those, I find its just easier to start the mission over if you start on an island than decipher a couple hundred number strings.