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And I just checked and repositioning the nav in the spine using simple drag and drop in Sigils' BookBrowser window, does in fact properly reorder the spine by verifying it in the opf. The re-ordered spine version of the epub can be saved and reloaded and its position remains where I put it.
So Sigil is currently working exactly correctly. So please explain exactly what you are doing step by step in Sigil that causes the nav.xhtml file to be moved back to the top (as you claimed). Is your epub3 opf broken in some way? Does it not properly add the nav property to the manifest?
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