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Using Split at Cursor just above the H1's in your single file epub works okay for me in the latest source. The filenames are added and are correct. I don't think anything in split changed since 0.6.0 but we'll re-test.
Now if you use just the code fragment in your post (the one without the id=Link_One in it), then when you split the filenames are not added - this is because the href points to a non-existent link so it can't find it again to re-link it. But this doesn't seem to be your issue.
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