I save the map to a file, for a custom story known as "Maps" folder. I check inside it after saving the map "Save As" to that location but its not there.
I restarted level editor, tried everything. Any solutions?
Amnesia only saves pre-existing maps.
Save it FIRST to the desktop first then drag and drop it to your maps folder.
And then when you load to map up from the map folder you can save it there from now on.
You should be able to save the file directly into your folder if you start the LevelEditor as administrator. Sometimes the privileges aren't allowing it to save there.
If you're using a Windows PC; right click your Amnesia folder (Amnesia - The Dark Descent or your redist, it doesn't matter), and open Properties.
Under the Security Tab, change the permissions for user (and Administrators) to have Full Control, and apply that setting. That should give you all the permissions you need to save in the Amnesia folder.