If you want to check that Pandoc is correctly found by rmarkdown, you can run
rmarkdown::find_pandoc()
This will tell which Pandoc will be used and which version. Pandoc is shipped with RStudio so there should be not issue with Pandoc installation itself.
This error could happen if some files is not found by Pandoc when doing the conversion. This could happen on Network drive, in some weird situation when doing parallelize rendering or when there is something of with one of the resource file. (images, ...)
This is highly dependent on your special situation. Can you share content of the document ?
Just a precision: This folder is not containing Pandoc binaries, but just rmarkdown resources related to Pandoc use. Pandoc is installed with RStudio and not rmarkdown. You can also install it yourself on your system if needed.