Close WindowController Without loosing Data in objective c

Question

So i have a windowController which i pop up using NSApp this window is called from mainWindowController.

ScriptSettingWindowController *mySettings = [[ScriptSettingWindowController alloc]initWithWindowNibName:@"ScriptSettingWindowController" owner:self];
    [NSApp runModalForWindow:[mySettings window]];

There are other UIElements which gets displayed only when using Owner:self. When using owner:self it takes over mainWindowController.

enter image description here

When i close the NSApp The control returns to the mainWindowController. But ends up crashing the application. I believe the control has to be returned back to mainWindowController before closing the NSApp.

To close the modal i use

[NSApp stopModal];
[NSApp orderOut:self];
[NSApp close]; 

but they do not close the popup.

[[self window] close];

[[self window] close]; this does close the window along with some variables being cleared and crashing the app.

Im dealing with an old project here and have no clue about mac development. Any help would be appreciated. thanks in advance