Q: repair bootcamp after creating new partition

I have a USB installer created through BC Assistant.  It doesn't seem to allow me to do Windows Startup Repair.  However, I have a USB installer created on a friend's PC using the Media Creation Tool.  It does have the Repair menu.

Was your W10 an upgrade from W7/W8.1 or a clean install? Does your 'friend's' USB allow you to boot the Mac?

If you compare the directory structure of the two USBs, there are Apple-specific drivers in $WinPEDriver$, which assist during boot. The MCT-based USB will not have this directory.

Clean install.  You are correct about the difference in the directory structures. 

I booted the BC Assistant-created USB drive, selected the drive titled 'windows' (not EFI Boot) and proceeded through the dialogues, looking for the repair functions.  In the process I inadvertently installed a new copy of Windows 10 to the Bootcamp partition.  This appears to be functioning properly and the previous install was moved to windows.old.  The shared drive is visible and writable from both OSX and Windows.  There are now two 'windows' drives to choose from at startup after holding alt/option.

Does System Preferences -> Startup Disk and Control Panel -> Boot Camp allow you to switch back and forth?

Do you see only one Windows drive in System Preferences -> Startup Disk, but two in Alt/Option?

Switching back and forth works.  Correct to the second question.  One Windows drive under Startup Disk, two in Alt/Option.

I've removed the windows.old folder using Disk Cleanup in Windows, but that had no effect on the Alt/Option situation.

You should have kept Windows.old. It allows you a rollback. The two entries are coming from the EFI Boot in the BCD. The incorrect one can be deleted. Please ensure that use bootrec.exe /rebuildBCD and and delete the non-existent entry. You can verify the hard disk path in the BCD.

LonerT,

I'd like to follow up on this discussion from two months back... I was never able to get the second entry removed using rebuildBCD.  I'm not very familiar with that utility and the solution wasn't immediately obvious.  However, everything else was working fine so I decided to ignore it and get back to actual work.  Subsequently, when I upgraded to macOS Sierra this week, the functioning Windows entry is now gone, only the non-functioning one remains, and I can no longer boot Windows.

Any help on sorting this out would be greatly appreciated!

You may want to run rebuildBCD and then use BCDEdit to remove the invalid entry.

RebuildBCD returns a result saying it finds no windows installations.

Are you running Bootrec.exe on C: or the boot disk X: from which you booted?

C:

On C: can you run

dir/s/p BCD

dir/s/p bcd*

You have a SHARED partition. Can you post the output of

sudo fdisk /dev/disk0

$ sudo fdisk /dev/disk0

Disk: /dev/disk0 geometry: 60821/255/63 [977105060 sectors]

Signature: 0xAA55

         Starting       Ending

#: id  cyl  hd sec -  cyl  hd sec [     start -       size]

------------------------------------------------------------------------

1: EE 1023 254  63 - 1023 254  63 [         1 -     409639] <Unknown ID>

2: AC 1023 254  63 - 1023 254  63 [    409640 -  537818704] <Unknown ID>

3: AB 1023 254  63 - 1023 254  63 [ 538228344 -    1269760] Darwin Boot

4: 0C 1023 254  63 - 1023 254  63 [ 539498104 -   95441288] Win95 FAT32L