I've fixed the same problem by running
DISM /Online /Cleanup-Image /RestoreHealth /source:WIM:C:\Users\User\Downloads\Install.wim:1 /LimitAccess against an updated
Install.wim with the latest Windows 10 Cumulative Update slipstreamed (KB3081452 and KB3095020 at the time of this post). There's no need to repackage an .ISO.
Basically, I followed the "Add updates to customized Windows" guide from Microsoft itself:
Dism /Mount-Image /ImageFile:"C:\Images\install.wim" /Index:1 /MountDir:C:\mount\Windows
Dism /Add-Package /Image:C:\mount\Windows /PackagePath:C:\MSU\Windows10-KBxxxxxxx-x64.msu /LogPath:AddPackage.log
Dism /Unmount-Image /MountDir:C:\mount\Windows /Commit
Those who don't have a copy of the original un-encrypted
Install.wim file may find this and this helpful.
Updated, I did another in-place upgrade on two other household PCs, Windows 8.1 -> Windows 10 x64, using the Media Creation Tool and the "Keep nothing" option. After installing all updates (including the latest cumulative update KB3093266), both PC failed the
"sfc /scannow" test and the
"dism /Online /Cleanup-Image /RestoreHealth" recovery, same error
So, I repeated the procedure described above, this time using a Windows 10 ISO from TechBench and slipstreaming the KB3093266 MSU into its
install.wim. Problem fixed.
Updated, the issue re-surfaced after upgrading to Windows 10 Version 10.0.10586.0 (November 2015 Update + latest cumulative update). This time, I simply downloaded the latest ISO from TechBench, mounted it and executed
DISM /Online /Cleanup-Image /RestoreHealth /source:WIM:E:\Sources\Install.wim:1 /LimitAccess, then
sfc /scannow. Apparently, there's no need to slipstream the latest cumulative update.
Updated, the issue re-surfaced once again on a different PC. This time I coudn't find the ISO (has TechBench gone?), so I had to use the Media Creation Tool, create a USB drive installation, then convert
dism /export-image /SourceImageFile:d:\sources\install.esd /SourceIndex:1 /DestinationImageFile:c:\temp\install.wim /Compress:fast
Then repair the image using Windows Update as backup (i.e., without
dism /Online /Cleanup-Image /RestoreHealth /source:WIM:C:\temp\install.wim:1.
Then repair the system files: