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I checked the code. Unfortunately it is not the library for generating the ePUB itself...
It is a bug I thought I fixed a long time ago, but apparently it is back again or it was my imagination. The last file will not have an entry in the NCX, so that means that if you do not automatically split the files during the generation, the NCX will be empty. If you do split, you will miss the last entry. Of course, the chapter is also missing the NAV document...
So, there will be an update soon for 1.x branch with a fix for this and some other functions that were already in the pipeline. It will not be the big update planned of course, but I feel this is too important.
In the meantime, I know that Sigil can recreate the NCX to fix this without manual interaction.
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