Here is my emulators.cfg file
lr-beetle-pce-fast = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-beetle-pce-fast/mednafen_pce_fast_libretro.so --config /opt/retropie/configs/pcengine/retroarch.cfg %ROM%"
default = "lr-beetle-pce-fast"
lr-beetle-supergrafx = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-beetle-supergrafx/mednafen_supergrafx_libretro.so --config /opt/retropie/configs/pcengine/retroarch.cfg %ROM%"
lr-fbalpha-pce = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-fbalpha/fbalpha_libretro.so --subsystem pce --config /opt/retropie/configs/pcengine/retroarch.cfg %ROM%"
lr-fbalpha-sgx = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-fbalpha/fbalpha_libretro.so --subsystem sgx --config /opt/retropie/configs/pcengine/retroarch.cfg %ROM%"
lr-fbalpha-tg = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-fbalpha/fbalpha_libretro.so --subsystem tg --config /opt/retropie/configs/pcengine/retroarch.cfg %ROM%"
You should probably trim it down, since you don't have installed all the emulators there.