Hi,
since I'm using the KoboTouch driver there is no differentiation regarding the extension. What I did is the following:
{formats:'contains($, "PDF", "PDF", "Books")'}/{author_sort} - {series}{series_index:0>2s| | - }{title}
Since I have PDF files only as a fallback if I have no EPUB (and for those scientific articles), I can safely assume that if the list of book formats contains PDF then there is no other usable format. So I simply decide on that where to place the respective book...
Btw., I have the impression that with this change the KoboUtilities plug-in doesn't work correctly, but I have to follow up on that.
Cheers and thanks, Joe