Hello!
I just had the problem:
1. epub2 converted to epub3 and then edited and re-structured
2. epubcheck plugin run on it--after some other errors mended, some were persisting--all related to toc.ncx (inherited from epub2 stage)
3. I finally understood that toc.ncx
wasn't being automatically updated--manually generating it again ended the trouble.
Well- I am not grumbling: as toc.ncx isn't mandatory for epub3, it makes sense--sort of. Only, I found the error reports highly puzzling until I tumbled into the explanation...
By the way: thanks for Sigil and its plugins
