I have noticed that Sigil has trouble when it can't find a file.
This can happen when you delete the file or what appears to be happening in your case, when it standardized the epub structure.
Quote:
See <a href="./ch01.html#CH01-91">note 1, on page 50</a>.
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I have a feeling the dot slash (valid) threw it off. on import.
HarryT probably has the easiest answer/work-around