Personally, I just download the patch to my phone and use 7Zipper 2.0 to unzip the file and use the FTP server to wirelessly put the patch onto my 3DS. Takes a bit of time, but it works. Hope I helped.
I had the same issue. If you're getting that message after installing B9S 1.2 and you're booting up your console with Luma 7.1, get the Luma 8.0 boot.firm and put it on the root of your SD card. Fixed it for me at least.
yo guys the sonic x shadow generations trailer dropped today, and shadow just straight up decided, and i hate (love) to bring this dead meme up, but, it's morbin time