It seems that the purpose of the update has been identified by eagle-eyed members of the Nintendo Life community. The previous update removed the overall total figure in the counter for puzzle pieces collected, and now it's back. Photographic evidence is at the bottom of the article, thanks @Greenalink!
It's time for the mystery 3DS update game, everyone! There's a fresh software update for StreetPass Mii Plaza in Europe, which has a whizzy download bar like a system update, yet we're not sure what it does. It's a thing alright, we know that much.
The update — now version 3.2 — may simply be to improve stability and security, as no obvious changes are there to be seen. Even after the update the DLC Bunny still has the annoying habit of only telling you about the combo pack pricing when you do a specific order of answers, for example, rather than right off the bat.
We'll assemble a crack team of software experts to figure out what the update's done, and at the time of writing it isn't available in North America; the region will need to wait a little for the delights of version 3.2.
Thanks to MK II for the tip.