Missing Files or File System Corruption after using Partition Outside of Windows

Problem:

After booting back into Windows, file changes made to a partition outside of Windows may be missing or the file system may be corrupted. Running chkdsk /f on the partition may either find or remove the modified/added files as well as find other file system errors.

For example, a backup image is created outside of Windows (e.g. using Image for Linux). When booted back into Windows and chkdsk is run (automatically, in some cases) on the drive containing the backup, the image file is missing; or, the image file originally didn't show up on the drive and does after chkdsk runs.

Cause:

This problem can be caused by hard drive accelerators (e.g. Lenovo's RapidBoot HDD Accelerator) as well as the Windows 8.x/10 Fast startup feature. The file system on the drive becomes corrupted when modified outside of Windows due to cached data being used upon booting back into Windows instead of the actual (modified) data on the drive.

Solution:

Hard drive accelerators

If a hard drive accelerator is being used, uninstall or disable it and check if the problem persists.

Disable Windows 8.x/10 Fast startup

Use one of the methods below to disable the Fast startup feature:

Using Windows Settings / Control Panel

1. Press WinKey+X (or right-click the Start button) and select Power Options from the Quick Link menu. 
   
   
2. If using Windows 10 1703 or later, the Power & sleep section of Settings will open. Click the Additional power settings link to open the Control Panel. 
   
   
3. Click the Choose what the Power buttons do from the links on the left. 
   
   
4. Click on the Change settings that are currently unavailable link (located in the top area). 
   
   
5. Remove the checkmark from the Turn on fast startup (recommended) option under Shutdown settings.
   
   
6. Click the Save changes button.

Using TBI Notify

If TBI Notify is installed, it can be used to disable Fast startup as well as warn if it's currently enabled (Windows 10 upgrades usually re-enable it). By default, TBI Notify is installed with Image for WIndows.

1. Right-click the TBI Notify tray icon and select Settings from the menu.
   
   
2. Click the Disable Fast Startup button. (This button is only available if Fast startup is enabled.)

Using BootIt BM or BootIt UEFI

1. Boot into BootIt BM or BootIt UEFI. 
   
   
2. Click Partition Work on the desktop. 
   
   
3. Select the Windows 8.x/10 partition and then click the Properties button. 
   
   
4. Click the Disable Fast Start button.