When you disconnect from GitHub Enterprise Cloud, the GitHub Connect GitHub App is deleted from your enterprise account and credentials stored on your GitHub Enterprise Server instance are deleted.
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In the top-right corner of GitHub Enterprise Server, click your profile photo, then click Enterprise settings.
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In the enterprise account sidebar, click GitHub Connect.
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Under "GitHub Connect", to the right of the enterprise account you'd like to disconnect, click Disable GitHub Connect.
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Read the information about disconnection, then click Disable GitHub Connect.