Windows fails to boot - fixmbr, fixboot, bcd (MBR disks)
Date Added: 8/24/2018

NOTE:
This entry is for disks formatted as MBR, not the newer GPT format.  If you are still using an MBR disk, you probably should ignore this entry and reformat the disk to GPT instead.  There's another Knowledgebase article about that.  Windows 10 no longer supports MBR disks and you will not be able to install the latest Windows Updates anymore unless you switch to GPT.

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I used MiniTool Partition Wizard to clone a HDD to a new SSD.  The new SSD worked well except I noticed that Partition Wizard did not set the partition alignment correctly (at intervals of 4096KB).  So, I booted Partition Wizard from the free ISO and clicked the button to automatically align the partitions.  After that completed, my Windows 10 would no longer boot (but the partitions were aligned correctly this time).

There is likely a shorter way to fix this issue, but here's what worked for me:

1) Boot from a Windows 10 installation flash drive or DVD
2) Select Repair your computer
3) Troubleshoot
4) Command Prompt
5) bootrec /fixmbr
6) bootrec /fixboot
7) bootrec /scanos
8) bootrec /rebuildbcd (this failed for me, so I continued)
9) diskpart
10) select disk 0 (or whichever disk has the OS and EFI partitions on it)
11) list vol
12) select vol 2 (or whichever volume has the 100MB FAT32 EFI partition)
13) assign letter=y: (or some unused letter)
14) select vol 4 (or whichever volume has the OS installed, probably the largest partition)
15) assign letter=c:
16) exit
17) cd /d y:\EFI\Microsoft\Boot
18) bootrec /fixboot
19) ren BCD BCD.bak
20) bcdboot c:\Windows /l en-us /s y: /f ALL
21) exit

Remove your flash drive and reboot the computer.  It should boot straight into Windows, as usual.

source: https://neosmart.net/wiki/fix-mbr/#Fix_the_MBR_in_Windows_10

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