Thanks for the quick reply, Yes you were correct, sourcemaps was messing up the debugs.
I found the problem, First of all, I thought when call
deletingObject.destroy({ children: false, texture: false, baseTexture: false });
All the children will be still visible on the stage, but little bit digging make me realise that when you delete the parent all the child objects will have null parents hence it won't show on the stage. so it wasn't any bug just me been not fully understanding the scene graph. Anyway, I manage to fix my problem simply by getting all children and setting their parent to the current grandparent.
onDestroy = function () {
// Get all the children
for (var i = 0; i < this.children.length; i++) {
// Reset the parent
this.children[i].parent = this.parent;
}
// Destroy this object
this.destroy({ children: false, texture: false, baseTexture: false });
}