Hi!
I've just managed to remove the "Update popup" from my 3DS by simply renaming a file on the 3DS SD card.
In my case, I'm on version 9.2.0-20E and I got the update after leaving the console in sleep mode on Saturday.
Today I did a search on the SD card (on my computer) looking for modified files dated on Saturday. The good news was that there were only three files modified that day, all the same time.
The files were the following:
- F:\Nintendo 3DS\c700e9d4efe53c49f7d5d00e2d60ff4f\19d200c73110b71a3030303000284245\extdata\00000000\00000228\00000000\00000007
- F:\Nintendo 3DS\c700e9d4efe53c49f7d5d00e2d60ff4f\19d200c73110b71a3030303000284245\extdata\00000000\000002ce\00000000\0000001a
- F:\Nintendo 3DS\c700e9d4efe53c49f7d5d00e2d60ff4f\19d200c73110b71a3030303000284245\extdata\00000000\00000229\00000000\00000003
The biggest one (the first one, ~17.5MB) seemed to be the system update, since it was the one I renamed and made the popup disappear.
You can repeat the steps I did if you know when you downloaded the update or you can also test (under your own responsibility) to rename the same file as mine (if it exist on your system). If you rename the file you can always set it's name back to the original, or even better, make a backup of the whole SD before doing anything.
Hope it helps!