The centred bold text is almost certainly BD making it into a (very long) title (or possibly subtitle). I've had this problem occasionally. Check by going to 'tools' then 'element browser' and look for titles (then subtitles). You can correct it by selecting each paragraph and reassigning it as a paragraph.
This sometimes takes ages, but is probably responsible for a lot of the TOC problems.
You may well find it faster to take Steve Jordan's advice.
I don't think the size should be the problem: I've made 5 Mb books.
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