Oh, it's quite simple.
Save files from your Flash Cart can be used with DeSmuME using the Import/Export Save options under the File Tab. Using the .sav files, open them up in PokeStock, Grovyle's Mystery Gift Editor or PokeSav, then add the Wonder Card .pgf (or .pcd?). Save the file, import it in DeSmuME, and collect it from the Event Guy.