I'm experiencing this issue. Bookdown knits without errors, but only the index.Rmd file is rendered correctly into an HTML page.
When I inspect the _book directory, I find HTML files that correspond to the Rmd input files, but they are all zero bytes in size. For example:

I first encountered it when attempting to create Bookdown output with my own files. But, as the screenshot above shows, it also occurs with the "Minimal Book Example" boilerplate created when setting up a new Bookdown RStudio Project.
It has persisted even after reinstalling the bookdown package and reinstalling RStudio itself.
Mac OS 10.13.5
R 3.5.0
RStudio 1.1.453
Bookdown 0.7