Correctly replace scene root when `must_reload` in `EditorData::check_and_update_scene()`

We need to update the scene root in multiple singletons to ensure that
certain flags are correct. This is what `EditorNode::set_edited_scene()`
does.

Usually we use `replace_by` to complete the replacement of the scene
root. Call `EditorNode::set_edited_scene()` when the `replacing_by`
signal is emitted to set the new scene root. This is suitable when
using a single node to replace, which may be problematic if the
replacing node is a tree. Because during the call to `replace_by()`,
the new node and its child nodes will enter tree during `parent->
add_child(p_node)`, and later emits the `replacing_by` signal.

When the parent scene has to be reloaded because the child scene
changes and switches to the parent scene, there is no need to use
`replace_by()` since the scene's diffs are already saved.

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