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You have to push the Generate toc button after you do the split to update the NCX. Sigil will not update it for you. Remember, users now have the ability to edit the NCX by hand and Sigil cannot assume you want your TOC overwritten.
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This is very interesting. I have finally experimented with a file to see when the toc.ncx automatically updates and now understand how you put things together.
Since looking in detail at the toc.ncx, it would seem that the only changes that can be made is to the TEXT entry and the sequence. Changing src would seem wrong but can be done. Trying to use to force an indent doesn't work.
Also version 4.0 loads the first files (title page, and table of contents) out of sequence and when I move them into proper sequence a "push" of the Generate toc button is needed to update the toc.ncx.
It would seem that a better approach for the user is to have a "do not update toc" button and otherwise use full auto update.