I have an Rmd file that has quite a lot of top level (# etc.) sections. I'm only getting about 8 in the pdf.
I have built a "small reproducible example" and have also tested by using
library(knitr)
knit("mytest.Rmd")
The .md file is OK. I've then tried pandoc to convert md to pdf and the problem is located there.
I realize this is a pandoc problem, but seek pointers to where I can notify of this bug, and also make sure the Rstudio community is away of it so there are not too many reports and effort can be focused on fixing the issue.