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This is because they have to check your A records and generate the certificate and from my observations that happens when you add the custom domain.

After I've set the A records, I removed the custom domain from GitHub's Settings and then re-added it.

It started working afterwards.

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I did that, and still not working. After setting A records, re-entering custom domain and waiting for few minutes, I get this message in Settings of GH-pages `Domain's DNS record could not be retrieved`. Bummer. Maybe I was to eager to remove Cloudflare from the equation.

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