Use a newer FTP
FTBrony is outdated. At least that's the old name of it which has been changed for quite a while.
Either that or take the SD card out of the 3DS and access it right from the computer.
Just tried FTPDB, but I'm getting a similar error:
/JKSV/Saves/Pokemon_Omega_Ruby: 138 Illegal byte sequence
550 unavailable
I know this might be the wrong place to troubleshoot FTP problems, but I was wondering if I was doing something wrong in JKSM. And you're right, I could just pop my SD card into my comp, but transferring small files over FTP would be super convenient.