Many years ago, I was getting very strange behaviors with an SD card. The first problem I noticed was an unexpected error during a data update that prevented the update from completing, but did not seem to affect iFly performance when the SD card was returned to the 720. Eventually, I think I tried to format the card, and rebuild it from scratch (with help from iFly support), and in the end the AP guys suggested that it might be an issue with the card itself.
I ended up trying to rebuild the iFly dataset on a new SD card, and that worked fine.
Even though I'd been using the original card for a couple years by that point with no issue, either something on it failed or else the size of the dataset reached a point where it was trying to write to an area in the card that held a latent failure that was finally being exposed. Either way, I retired that card and continued using the replacement.
In your case that seems unlikely, since if I understand your situation you first saw this error when trying to clone your original SD card to a new one, and now you are seeing it when trying to perform a data update on the original card, so that would mean that two different SD cards have developed an issue.
Still, it's all I can think of.