The following guide explains how I fixed the error "We couldn't install Windows 10. The installation failed in the SAFE_OS phase with an error during BOOT operation".
I tried to upgrade a system running the RTM version of Windows 10 to the newly released Threshold 2 build. I have done so numerous times on other machines and never ran into issues before.
This time was different however as the following happened: Windows Update picked up the new version just fine, it would download it and start with the installation.
After the reboot it would display a modified troubleshooting page with options to shut down the computer or open advanced troubleshooting options. Regardless of my choice there, it would load the old desktop afterwards reverting all the changes made during installation.
What weighted even more was that Windows Update would not list the new update as available anymore afterwards. Thankfully, I had already posted information on how to install the update to version 1511 if Windows Update would fail to display it.
The only option that you have then is to download a program from Microsoft that you get on this website and run it to upgrade.
Anyway, I tried that and it resulted in the same issue. Research on the Internet revealed that I was not alone, but most topics were about previous versions of Windows and attempts to upgrade to Windows 10.
The solutions did not help in my case which meant that I had to find the solution on my own.
The main hard drive of the computer was encrypted, and while I never experienced any issues in this regard during upgrades, not even from Windows 7 to Windows 10 for instance, I decided to turn off the encryption and attempt the upgrade again.
Turning off the encryption is not as simple as it sounds as I had to decrypt the drive. Thankfully, it was a fast Solid State Drive with only 256 Gigabyte of space which meant that the process completely quickly enough.
I ran Microsoft's upgrade tool again and after some waiting and praying, it turned out that turning off encryption fixed the issue.
The Windows 10 upgrade was installed on the system, and the first thing I did, after modifying preferences that the upgrade reset and changing some default apps, was to encrypt the drive again.
The error may not be that common but if you run into it and use encryption, you may resolve it by disabling encryption for the time of the update.
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