[Trevally.]

editor locations.mis are map marker only and is not the actual harbour.
The harbours are objects placed in your game and will be there in all single missions.
If you want to move or change a harbour - you must use the object editor to do this.

Also - if you are making missions with more than one layer - it becomes a campaign project and thus can not be saved as a single mission

Where you do want to use layers in single mission - you can open the .mis files with a text editor and merge them into one file. This can then be saved as a single mission.