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Help SD card is damaged

This weekend I got a "SD card damaged - you may have to reformat it" error on my Optimus V.

I was able to read it on my PC and copy everything over, but.. I use Link2SD due to the lack of app space on the phone, and I'm worried that if I format, I'd lose all of those apps and their data.

I'm going to try to scan and fix the disk, but assuming that doesn't work, is there a way to only format the non-app partition? I don't know which partition is actually causing the problem, but I think it's the non-app partition because my widgets aren't showing up on my homescreen, nor on my lockscreen - none of them are linked to the SD. Also, my camera app won't take photos because it doesn't recognize the SD card.

Any suggestions? Any way to pinpoint which partition is bad? Can I just delete the non-app partition and create a new one in its place, then copy over my backed up files, or will the card still be bad?

Info: Rooted Optimus V running Harmonia 1.3.
 
According to a vm rep. Some of the v's have a bad sd card reader. I got my phone replaced for free because of that
 
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