My mistake. I assumed this was default behavior as of Sigil 0.9.16 when we made the ncx optional. But I see that's not the case. Sigil 0.9.18 DID update the optional ncx of an EPUB3 whenever a file was renamed, but 0.9.991 does not.
Sigil DOES still update the ncx of an epub2 that is in Sigil's standard format, but not one that uses an alternative structure where xhtml is not in the "Text" subfolder.
We'll look into it. This is exactly the type of thing that the pre-release was intended to ferret out. Thanks!
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