This is by design (right now). As you've seen, changing an id breaks the tree as child nodes no longer reference an existing node. You'll have to go through the file and update each place where the id is referenced.
There's a few reasons why I didn't implement this (yet): it is complicated and risky. The main reason is there may be places where an id sits, but I don't know about it (in particular: specific properties with an id, other external files, or even unknown chunks). If I'd update the places I know about now, you'll run the risk of having the file only partial updated. Inexperienced modders will assume 'all is good' and there the trouble starts. At least now you know there's a manual fix up to go through.
So, it is up to the modder to rebuild a tree structure chunk by chunk (node by node) where changing id's is involved.
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