copy the ExtractedExeFS folder file back to your decompressed game files, then delete the "code.bin" file there and rename the ".code.bin" by removing the "." (dot). Then rebuilt your game. Remember to keep a ".code.bin" file (file with the "." (dot)) PK3ds cant modified shop item without the (dot).
pk3DS: Pokémon 3DS ROM Editor and Randomizer
in ROM - 3DS Research and Development
Posted
So does this also fix the ground items + the TMs?