A while ago I had the same problem, but after some long research I discovered a great program called GetDataBack. It helps you recover files even if your pc doesn't recognise your SD card. Just copy your files to your pc, reformat your SD card and put everything back on it. You might need to do some renaming though, some file/directory names will be messed up.
And a small note, you have to pay for the program but if you don't want to go through the hassle, there are some cracked versions out there
