If you add a duplicate reflist to a page, VE will happily display it and then save it to the wikitext. But the read view ignores it completely. If a user tries to add a duplicate reflist, we prevent it with an error to avoid confusion in the rare cases this comes up.
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The problem with this is that inserting a new reference list will clash with an existing neutral one initially, but not once you set it to track a different reference group. Prompting the user to fix it before they save (but not stopping them from inserting a duplicate one) would be needed; not sure what kind of design that would need.