Thank you for the reply! I do not have a backup of the USB. I did as you said and shutdown Unraid, popped the USB into my PC and then windows recognized there was an error; it scanned and repaired. As for backing up the USB, I copied all the content from the Unraid USB into a folder on my desktop. Is this the correct way of doing this?
I was able to boot everything fine. It would take a few minutes before the warning pops up, but either way I will report back later with an update.