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I found the solution! The setting isn't in the main "Settings" tab for the repository. It is managed under the GitHub Copilot specific administration area within the repository settings.
Here is how to do it:
Navigate to your repository's main page.
Click on the Settings tab.
In the left sidebar, scroll down and click on GitHub Copilot under the "Code and automation" section.
There is a setting there to "Enable GitHub Copilot" at the repository level. Uncheck this box.
Click the Save button.
This overrides the organization-level setting just for that single repository.

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Answer selected by Ganim03
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Question Ask and answer questions about GitHub features and usage Copilot in GitHub Copilot functionality in GitHub Copilot Chat and in github.com
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