Sorry for the English, I use a translator.
I confirm the problem. More details:
If you do not float away from the freeport square, the game is saved and loaded correctly. If you cross the border of the square, exit the game and re-enter, at the loading stage the ATLAS\ShooterGame\Saved\SavedAtlasLocal folder will be cleared and the game will start over.
There is a solution found in this thread: https://www.playatlas.com/index.php?/forums/topic/120617-patch-52608-customization-update/&tab=comments#comment-525665
The solution is: you need to put a "?Version=1" to the end of the "lastgridcord" file, because probably its missing in your case too.
If your lastgridcord file contains only: ServerX=7?ServerY=3?HomeServerX=7?HomeServerY=2, then you will start over and over with new char, etc.
Its a wrong one. But, if your file contains the ?Version=1 string at the end, something like this: ServerX=7?ServerY=3?HomeServerX=7?HomeServerY=2?Version=1, then you can continue your progress without resetting your singleplayer data again, and again, and again.
