I try to produce one PDF report split on sections based on a grouping variable, using brew and knitr. My grouping variable may contain special char
Since you are using UTF-8, which is not the native encoding of your OS, you need to explicitly tell knitr the encoding of your input document. For example, you have to call
knit2pdf(brew_out, encoding = "UTF-8")
But I'm not sure if brew can handle non-native character encodings. If not, I suggest you use your system default encoding (should be ISO8859-1 in this case), and
\usepackage[latin9]{inputenc}
Or do everything in knitr if you have to use UTF-8 (this also enables you to click the button to compile the document); see 075-knit-expand.Rnw for an example.