This has only been tested by myself on a small, old 3DS on 8.1, 9.0 and 9.4, but it's reasonable for this to work on any console. Feedback is obviously appreciated!

  1. Completely power off your system.
  2. Boot in recovery mode (press L+R+A+↑+Power, hold the first four about 1 second, more won't hurt the system but only your fingers... ;))
  3. It will ask you as usual to update. However, it will take a little longer for the screen to come up compared to the speed it would have had if you didn't already have an update.
  4. If you click yes, the update will be completely redownloaded then installed...
  5. If you click no, it will power off and you'll go home free!

Update 2017: Yes, this is only for sysnand (although you can hack the import.db of a nag-free sysnand's internal storage onto emunand through Decrypt9 or similiar ways, check out specific tutorials), because no CFW implements the launching of emunand's recovery mode!

This is also unrelated to the forced updates for YouTube or the browsers bundled with 9.9+, and neither it resets the "update available for this app" text
on the Home launcher!