If I make changes to the Linker script via the GUI in SDK (right click on the application and choose Generate Linker Script), these changes are not retained.
They default back to 1K (or whatever the previous value was).
How can I work around this?
You will need to change the Linker script (.ld file) in the application src folder in the Project Explorer in SDK.
Right click, and select Open with -> Text Editor.
In the text Editor, you can now manually change the stack and heap here: