dont worry about that, it just reset the drive letter
just make sure you know what physical drive has windows on it (ie the Seagate has the OS, and the Maxtor is the backup)
then merge the backup files and remove the "Maxtor" drive and put the "Seagate" as Primary Master (or Raid 0 if you into SATA) and it will boot
C:\ is not the first drive booted