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Re-importing some urls will synchronize any existing Info Items for the duplicate urls (if the option to skip duplicate urls is checked) but will also ensure the duplicate Info Items are linked where they are imported. So in your case, the duplicate Info Items have become Logically Linked (linked to multiple parent Info Items). The original linkage you defined still exists but they are now also parented where you re-imported them.
You can verify this by viewing the contents of the Parents pane when one of them is selected (and by the presence of the link icon overlay over the item's icon).
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