Well you have two options for the H2testw, either running it with write+verify that would delete your data, or using verify only to check the card.
That... is not even remotely what I asked. The H2Testw is not a problem right now. What I'm wondering is, say the SD Card comes out alright, and detects no problems. I'd still be in the same position where I started. Would I need to clean the SD Card and follow the Finalizing Setup part again? And, I wouldn't need to copy the "Nintendo 3DS" folder back, right?