This is similar to the recent issue posed by jtr13 where the order of sections in the page sidebar have changed, however I'm missing sections from the page entirely. Rmd files 02- though 09- don't have their respective html files showing up.
I've installed and rerendered using 0.10 and the developer version on GitHub, but haven't seen the page (being hosted on GitHub) update.
I've resolved the issue myself by looking more closely at the commit where the disappearance happened. In the middle of one of the Rmd files, I had placed:
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Other Variables
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to try to represent a new section with a horizontal rule without it being numbered. This was likely interpreted during the render as a new section/YAML and subsequently turned the later page sections into code confetti.