Bootcamp using chkdsk /b flags free space as bad sectors

Just purchased a new 2016 MacBook 12" with 512Gb SSD

Installed Windows 10 using Bootcamp and all appeared to be working okay. Let Windows 10 install the latest updates.

Then decided to use Winclone, a 3rd party tool, to back up the Bootcamp partition. Winclone recommend running Chkdsk /B beforehand to correct any disk errors.

This had the effect of flagging almost all the free space as bad sectors. Over 320Gb of free space was reduced to around 300Mb. After this happened there seemed no way of recovering the space. Running Chkdsk /b several times didn't change anything. Running the disk check in OS X said the disk was healthy. Couldn't find any 3rd party tools that would reset the bad sectors.

Eventually reformatted the Bootcamp partition and reinstalled Windows 10. Everything is now fine but can't risk running Chkdsk /b again.

Looks like some incompatibility between the hardware, Bootcamp and Windows 10.