San Disk Secure Access V2.0- Vault has disappeared?

I have a horrible feeling the new vault has opened over the top of the old one

Possible but hopefully not the case.

 If this is the case, is there anyway of getting those files back??

No, so lets hope that’s not the case.  With the USB drive inserted and SecureAccess not open from a Command Prompt try running CHKDSK on the drive.  Hopefully it will help the original vault to reappear.