Extracting from 3DS (HackingToolkit9DS failed)

I used HackingToolkit9DS to extract a game (Pokédex 3D, specifically), but of all the .bin files, only "DecryptedManual" got anything extracted from it. So I'm left with DecryptedExeFS.bin and DecryptedRomFS.bin unextracted, as well as no extracted banner.

Is there any way I can extract what I need from the leftover BINs?