On 10.3....Found out that was my problem, but now I'm still getting stuck at 'magic received, transfer beginning' or whatever. I'm trying to install Detective Pikachu and since I don't know how to make a .3DS into a .CIA even with the use of a tool, I found a CIA on 3DSISO. It's JPN but that shouldn't be a problem as I'm on emuNAND 9.2 and using FreeMultiPatcher to play some of my other JPN games like Assassination Classroom: Grand Siege on Korosensei, one of my favorite anime series as well as games. I'm running unlinked NANDS that are both on 9.2 as I am afraid to update and have something go horribly wrong. The game itself is 680MB and I have 760MB where I am trying to install it (emuNAND) but NASA says you can install it directly so you don't have to worry about double space. I have maybe 290MB left on sysNAND btw.
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For updates you could just get the CIA from somewhere and install it using BBM or FBI, that's how I updated Smash and a few other games.