I found the problem! I forgot to call setIdAttributeNS(null, "Id", true); for
all id attributes in the xml document.
e.g.
NodeList allIds = findNodes("//*[@Id]", document);
for (int i = 0; i < allIds.getLength(); i++) {
Element id = (Element) allIds.item(i);
id.setIdAttributeNS(null, "Id", true);
}
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