Strange i was able to extract the save file even with normal Homebrew, i was really surprise to be honest. Infact ultil the recent Homebrew Update from smea it was impossible to extract the save file from the VC game Pokèmon. If i remenber correctly in the save editor there is an option for refresh the list of game installed on your system. Try that option is possible that the save editor have not detected the game on your SD.