There are some folders and files that are hidden inside the SD Card. The user cannot see it directly. If your files are hidden and you want to see them again, follow the following steps:
1. Goto My Files
2. Press Options and select more
3. Then press Settings
4. And enable Show Hidden Files
After that, go back to the SD Card and see if you get back the files that you found missing.
If you still can't get it, follow Undelete apps to get those files back.
P.S. I am a newbie.