Actually, I'm having the same issue four months later, so rather than start a new discussion, perhaps we can continue this one, since you're already on track.
I'm attempting to create a collection of experimental formalist poetry (a little of which you can see
here).
The book works and looks quite nice for the first four poems and then goes dark. None of the subsequent poems appear in Sigil. I haven't had this issue using the Office plugin mentioned before, but neither does the output look as clean as Sigil's.
Most of the poems have been published and some have been translated into seven languages so far (including Greek, interestingly), which means I'm not overly concerned about showing the file to someone who knows more than I.
But if there are tags in the way, how can I get at them without stripping the text and destroying the visual look of the book so far?