When upgrading Windows from one version to another, The setup process needs to make sure everything will work after the upgrade is complete. However, when the user gets to see that the application is not compatible with the new version, he may cancel the setup process. This is when you get Windows Upgrade Error 0xC1900209.

The user has chosen to cancel because the system does not pass the compatibility scan to install the update. Setup.exe will report this error when it can upgrade the machine with user data but cannot migrate installed applications.

To complete the setup, you will have to remove applications and software which are not compatible. Once those applications are removed, you will need to run the setup process again.

You can also use the Windows Assessment and Deployment Kit (ADK) for Windows 10 and install Application Compatibility Tools to investigate further.