Follow these instructions to transfer files from one SD Card to another. Be very careful that you do not alter the files in the "Nintendo 3DS" folder on your computer in any way.
Need: Two compatible SD cards or SDHC cards
Need: An SD Card slot on a PC or Mac or a commercially available SD card reader/writer
Do Not: Alter, move, or erase files in the Nintendo 3DS folder.
Do Not: Overwrite data by recopying to the same SD card.
What to do:
Generally speaking, it's best not to bump old threads. Instead, create a new one.
But to answer your question, it's likely the files were not transferred properly, as doing this transfer is somewhat risky.