3 more years have passed and pdfunite still keeps harassing its users. ($ /bin/pdfunite --version pdfunite version 0.62.0 Copyright 2005-2017 The Poppler Developers - http://poppler.freedesktop.org)
Both earlier suggestions (-o switch and error if output file exists) are fine. Just to rewake the motivation I add a 3rd one: print the output to stdout and it's up to the user to redirect it to whereever they wish. This could coexist with the -o switch. PK
