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If epub2, you should be able to simply select it in Sigil's BookBrowser and right click and select delete.
If epub3, if this file is not the required nav document, you should be able to do exactly the same thing.
If it is acting as the nav document under epub3, you may not delete it. You can manually remove if from the OPF spine, or just add linear="no" to its spine entry. Valid epub3 readers will then not display it as part of the book spine progression.
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