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GitHub is not allowing them to turn it back on yet (source: multiple people on both sides)

GitHub should insist on it being converted to a GitHub App before they allow it to be re-enabled.

That way org admins can see the requested permissions and control exactly which repos are permitted. GitHub OAuth apps are an absolute nightmare to audit or control.

They were using a legacy GitHub integration. Maybe it's inherently unsafe and they need to rewrite things using the new API.

Audit?