Default 'save as' folder cannot be changed

When I have a new file (i.e. new file in the editor, put contents in it and save) then it saves always to a certain folder. But I cannot change that folder.
I removed the ‘Project Manager’ package, but despite this, the default folder cannot be changed.
When I open “~/.atom/storage/application.json”, I see the wrong default folder in it and when I remove it from the list, restart Atom, then the wrong default folder is restored in “~/.atom/storage/application.json”. There should be a setting where this folder resides, but cannot find it in any settings.

How can I change this default folder of Atom ?