I had this happen... It wasn't a case of StorageCard vs StorageCard2. This was a case of the index becoming corrupted.
What I had to do was download an undelete utility from the web, put the MiniSD card in my computer and undelete the files.
Once the undelete was done I was able to see the files and folders again.
Moral of the story, backup everything once in a while just in case the index gets corrupted again.
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