First and foremost consider this:

• Only documentation related issues should be filed here. Not RetroArch bugs, or core bugs, or game bugs, or build errors.
• Before reporting a 404, refresh the doc a few times.

Documents

https://docs.libretro.com/development/retroarch/compilation/3ds/

Proposed changes

RetroArch on 3DS is statically linked. With statically linked RetroArch, each executable is a separate libretro core instead of the core being separately loaded from a single executable. A pre-existing libretro library needs to be present in the root directory in order to link RetroArch 3DS. This file needs to be called 'libretro_ctr.a'.

Where to make/get 'libretro_ctr.a' is never stated.

You ever figure this out? I'm having issues compiling RetroArch for 3DS and I believe this file to be the issue. I was told to compile a core to get this file, but the subsequent RetroArch build crashes immediately on launch.