Unable to install Windows Update KB in Server 2008 R2 Enterprise

I'd check the file versions system has versus those listed in KBs. If system has higher file versions then "not applicable" would be expected behavior.

https://support.microsoft.com/en-us/topic/microsoft-security-advisory-availability-of-sha-2-code-signing-support-for-windows-7-and-windows-server-2008-r2-march-10-2015-d1b1b28c-b7fa-2902-f5a2-dc533812df7a
https://support.microsoft.com/en-us/topic/servicing-stack-update-for-windows-7-sp1-and-windows-server-2008-r2-sp1-march-12-2019-b4dc0cff-d4f2-a408-0cb1-cb8e918feeba

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Hello

Thank you for your question and reaching out. I can understand you are having issues related to installing KB on Windows 2008 R2.

The most common reasons for this error are described in the following.

1. Update is superseded
   As updates for a component are released, the updated component will supersede an older component that is already on the system. When this occurs, the previous update is marked as superseded. If the update that you're trying to install already has a newer version of the payload on your system, you might receive this error message.

Check that the package that you are installing contains newer versions of the binaries. Or, check that the package is superseded by another new package.

2. Update is already installed

If the update that you're trying to install was previously installed, for example, by another update that carried the same payload, you may encounter this error message.
Verify that the package that you are trying to install was not previously installed.

3. Updates are published by CPU architecture. If the update that you're trying to install does not match the architecture for your CPU, you may encounter this error message.

Verify that the package that you're trying to install matches the Windows version that you are using. The Windows version information can be found in the "Applies To" section of the article for each update. For example, Windows Server 2008-only updates cannot be installed on Windows Server 2008 R2-based computers.

--If the reply is helpful, please Upvote and Accept as answer--