I think you are saying that you use flexdashboard by having an rmd that uses it, which generates a long html, and you take that html and host that on a pure html web hosting service ?
ok, I don't have a direct solution for you, but HTML is simply text, and R can be used to generate text and export it. I would probably make a HTML template that I wanted to populated for each country. Then have an R script that iteratively creates a page for a country based on that template and write it out as its own html file. and finally produce a contents page with url links to the generated pages.