The PCE VC for the 3DS made by Konami isn't that great because there were only five (5) games ever released for it in Japan. It's a bare bone emulator, so it's compatibility for other PC Engine and TurboGrafx-16 games is understandably horrid. However, the Virtual Console's GUI and user options are top notch.
If you want to play PCE/TG16, use
TemperPCE or
RetroArch.
***
For your second problem using 3DShell and FTP, this one's a mess to figure out what's wrong with it. I've had files on my SD card that appeared as missing when viewed in WinSCP client. You can try copying everything off your card onto a computer (
not using Teracopy but with Windows File Explorer),
quadruple reformat the card, add back everything (
again, with Windows File Explorer), and then see if the FTP issue goes way.