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:
select disk 0(0 is the number of the drive)
list partitionto see make sure this is the right drive and to find the system reserved partition number.
select partition 1(change 1 to the reserved partition number)
exitto close the tool
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.