I use knitr and rmarkdown to write vignettes for R packages. Thanks to the magic of pandoc it is easy to turn these documents into a variety of format
Two things:
you could 'include' the common content and have two source files with different headers, or,
if the extra vignette really doesn't show up in the index, write your own. From Writing R extensions: "At install time an HTML index for all vignettes in the package is automatically created from the \VignetteIndexEntry statements unless a file index.html exists in directory inst/doc. This index is linked from the HTML help index for the package." The vignette index entry might also be a clue to having your probably identically named vignettes be recognized as distinct.