I don't know about this error. But...
This error means that you started with a CXI file. The 3DS builder library I'm using for building decrypted 3ds ROMs needs a little more information than a CXI file has, so you'll have to use another option instead.
On this screen, I recommend "Build Luma Layered FS". If you're using Luma 3DS, just make sure game patching is enabled and paste the contents of the SD Card folder in the output directory onto your SD card. It should also work on Citra 3DS, although there's a chance you'll need to rearrange some of the files. See the Citra 3DS website for details.