Steps to reproduce:

• create simple Qt Quick UI or Qt Quick Application (simple Hello World) (Qt Quick 1 or 2 - does not matter)
• start debugging
• select 'Apply Changes on Save' (and maybe 'Show Applicatoin on Top')
• add a smaller and colored Rectangle to the main Rectangle and save (works)
• add another more smaller and different colored Rectangle to the Rectangle just added (does not work)
• add another smaller and different colored Rectangle to the main Rectangle (works)
• do the same for Text or other displayable content
• try to remove one of the (not) displayed items (warning comes up that this is not possible without reloading)

If you start debugging with already a smaller Rectangle inside the root and try to put a new children into it this won't be displayed as well.
It looks a bit like that only changes to the top level (new children to the root item) will be handled correctly.
Deleting of items is not possible at all (warning comes up for displayed items as well as for items that could not be applied on save)