You may try to run a check disk for the drives and let it repair them.
1. Click Start, type cmd in the Start Search box, right-click cmd.exe in the Programs list, and then click Run as administrator.
If you are prompted for an administrator password or for confirmation, type your password, or click Continue.
2. At a command prompt, type the following command, and then press ENTER:
Chkdsk /R X:
Note: In this command, X: is a placeholder that represents the drive letter of the volume that you want to check.
3. Press Y when you are prompted to check the disk the next time that the system restarts.
4. Close all applications, and then restart the computer.
Note: During the restart process, Windows checks the disk for errors, and then Windows starts.
5. After the computer restarts, repeat steps 1 through 4 for the other volume, and then rerun the backup operation.
For more additional information follow the link given below.
Check a drive for errors Check a drive for errors
If that does not help you may check the link given below which talks about the rebuilding of the Boot files run the rebuildBCD command and check if that helps.
How to use the Bootrec.exe tool in the Windows Recovery Environment to troubleshoot and repair startup issues in Windows How to use the Bootrec.exe tool in the Windows Recovery Environment to troubleshoot and repair startup issues in Windows