Sorry to dig out this old thread. I have a situation similar to this.
I have an external storage with 2 x 2TB ( Stardom 2Bay, JBOD mode ) that was working nicely with my Macmini .
Somehow since last week the disk is not readable anymore. I got the message that " The disk you inserted was not readable by this computer " and it asked to "Initialize", "Ignore" or "" Eject".
OS is the newest El Capitan (10.11.5) and I've tried other enclosure and docking station and all saw the same message.
I also tried multiple computers (MBAs, MB, PC Win 7) and got the same issue.
I then started trying to repair it on OSX Terminal: "diskutil list" showed me the disk is now disk3 without partition.
So I did this first: sudo diskutil verifyVolume /dev/disk3 and I got the error message: " Error starting file system verification for disk3: Unrecognized file system (-69846)" .
Then I used "sudo fsck_exfat -d /dev/disk3".
Now I got the message:
"Opening /dev/rdisk3 ** Checking volume. ** Checking main boot region. fsck_exfat: Invalid jump or signature Main boot region is invalid. Trying alternate boot region. ** Checking alternate boot region. fsck_exfat: Invalid jump or signature Alternate boot region is invalid. ** The volume could not be verified completely."
I then looked into TestDisk in Linux.
http://imgur.com/a/HoWrJThe picture was taken around 15% but I did complete the analysis.
But it seems like not recoverable.
I am trying to scan it with R-studio for data recovery now and found that the label is 00000000000000000000. The scan is still ongoing since it is doing slowly. But I think this might be related to your post regarding the broken VBR. However I don't understand how you exactly fixed the VBR.
Thanks for your suggestions.