I need to reformat my SD Card - Will copying be a problem

My SD card is acting quite odd. It takes a long time to load SD card games, Same with HBC, and the emulators aren't working. I want to copy the files, format it, and then copy back. Is there any problems associated with copying? I do have a lotta lotta VC and Wiiware on my SD card, and I don't know how those 000000000001 files will react.

There are absolutely no problems whatsoever with copying.

So no problems with the Ww/VC?

And the saves will still be there?

Sorry I'm being paranoid, I just got really really far into MajorasMask