You cannot have two template with the same filename

[pattiereaves]

If you have

// Prototype header.banner

and

// Prototype footer.banner

and they are in their own folders, i.e.

header/
 banner.html
 banner.scss
footer/
 banner.html
 banner.scss

and point to their own markup files with the same name, i.e.

// markup banner.html

it will use the same version of the file for both references (i.e. two versions of header/banner.html).