ECHELON is a top secret US spying network that intercepts and decodes electronic communications throughout the world. Originally conceived shortly after the second world war by the Five Eyes Alliance signatories (US, UK, Canada, Australia, New Zealand) to monitor Soviet communications, it has since expanded to encompass all forms of electronic communications globally.
First publicly disclosed by former NSA whistleblower Perry Fellwock in 1972, then subsequently by other journalists and whistleblowers such as Margaret Newsham, Duncan Campbell, Crispin Aubrey, John Berry, Nicky Hager, Mike Frost, James Bamford and many others.
Though general public awareness of the program is generally low even after it had been publicized for many years. In part due to government suppression in popular media with gag orders, harassment, and jailing of journalists and whistleblowers on espionage charges.
(The most recent whistleblower of this was Edward Snowden in 2015, under the codename "PRISM".)
The use of ECHELON in the story is only mentioned in the VN, since in the anime only the "main" storyline exists, and in a less detailed form.
In the VN, the method of transcending the 1.0% divergence is not simply to undo all of the D-mails, but rather to undo the fact that SERN ever notices the first D-mail, which requires Okabe to undo all (not mentioning side routes) the past D-mails to get the IBM 5100 back.
SERN notices the original D-mail through usage of the ECHELON system, which was checking for time-machine related content (or possibly Makise Kurisu related content, since the original D-mail contained nothing time or time machine related except for the future send date). The text content of this D-mail that was recorded by ECHELON was stored inside SERN's hidden IBN 5100 database, and had to be deleted in order to cross the 1.0% divergence.