Took me a while to figure this one out.

The reason for the error was insufficient space in the Windows System Reserved partition. I had to shrink my C drive and expand the System Reserved partition. (I used GParted from Linux, you can use a boot CD like PartedMagic or whatever method works for you).

Windows boot might break because of this. You’ll get error 0xc0000225.

You’ll have to boot from a Windows 8(.1) installation media, get to the command line and then:

1. Run diskpart
2. Type select disk 0 (0 is the number of the drive)
3. Type list partition to see make sure this is the right drive and to find the system reserved partition number.
4. Type select partition 1 (change 1 to the reserved partition number)
5. Type active
6. Type exit to close the tool
7. Run bcdboot C:\Windows (change C to the partition where Windows in installed).

Windows should boot now. You can use EasyBCD to remove the old unbootable BCD entry.

Hope it helps.