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In _simplenews_scheduler_new_edition() there's this:
// Store taxonomy terms to save later to the node.
$terms = $node->taxonomy;
// ... later
// Now save it as a new node.
node_save($node);
// Save taxonomy terms.
taxonomy_node_save($node, $terms);
node_save() will save the taxonomy terms anyway. There's no need for taxonomy_node_save() -- that's called by node_save() via the node api anyway.