In the article, he mentions using Evilgrade to do the backdooring. If you click though the link, you can find the README, which lists a bunch of applications that Evilgrade supports seeding backdoored versions of http://www.infobyte.com.ar/down/isr-evilgrade-Readme.txt
He likely just enabled them all, or at least enabled several which are likely candidates for his target to download.
Re:How I Hacked a Router
by stedaniels on Sunday April 06, 2014 @01:17AM
(#7539871)
Notepad++ checks a known URL for updates. He'll have spoofed the URL to tell Notepad++ that there was an update, his.
I suppose you could just serve up a fake backdoor program for every *.exe\msi download, and remove the honeypot on the second download? The first download would execute and maybe do nothing (or error) - prompting a second download which led to the real thing.