Lost my 3DS the other day. Despite having backup saves on another SD card, confirmed with Nintendo that while they'll be able to transfer all of my old games, the saves are unusable and lost forever.
Fortunately, most of my Pokedex is saved on the bank, but my Sapphire game had my battle maison team, a number of my legendaries, including event ones, and a decent number of level 100 in game guys I've had going all the way back to Emerald. Really sucks. I still need to review bank and see what I lost vs saved, but really unhappy about this situation, given how many years of cumulative work that is.
Follow up:
I redownloaded all of my games today, started a new save on Alpha Sapphire, and logged into Bank. Logging into Bank was effortless. After I had connected my NNID to the new 3DS, everything was set as far as Pokemon Bank was concerned.
I did lose a few things. My entire Battle Maison team, as expected. I lost a few level 100s that I had: a Venusaur and Aegislash from X. The Volcorona from Black. I also lost a couple old utility Pokemon I'd had forever - a catching Smeargle and pickup / HM Linoone.
I lost Celebi, Diancie, Shaymin, and a couple goofy experimental projects I was leveling up, like a highly leveled Shedinja and Wobbufet. I lost my 6 IV Japanese breeding Ditto.
The good news is, I had FAR more kept around than I had imagined. I still have....
99% of Pokedex completion.
All Dream World Pokemon from Black.
A full seven of my level 100 in game Pokemon across Platinum, Soul Silver, Black, Black 2, and X.
All Pokemon that I leveled up and trained in Join Avenue from Black 2 (about 18)
All shinies (6)
All carefully caught, or otherwise surplus legendaries still hanging around.
All things considered, this loss is basically nothing. Getting my Battle Maison team back will be almost effortless. I still have almost everything of substantial or sentimental value. I must have kept more things in Bank than I had realized. Even losing the Smeargle isn't that big of a deal....I'll be able to raise a better catching Pokemon without much trouble.
I am SO HAPPY with this outcome! Thanks, Pokemon Bank! I probably won't have the energy to play Sapphire again right away, but at least I won't be discouraged from the series when Delta Z comes out.