Once a certificate is published to public CT logs, you can’t remove it from them. However, if you chose to keep a certificate out of public CT logs and then discover that you need it logged, you can fix the situation.
To get an unlogged public SSL/TLS certificate into public CT logs, reissue the certificate and uncheck the Don’t log this certificate to public CT logs check box so we can log it. The resulting reissued certificate will be logged in CT logs. The browser warnings will go away once you install the reissued certificate.
Changes to reissued certificates don’t affect previously issued certificates
When you reissue a certificate, any changes you make to the reissued certificate don’t affect the original certificate (or previously reissued certificates). Changes only affect that reissued certificate and all reissued certificates going forward.
For example, if you order an SSL/TLS certificate and you choose to keep it out of public CT logs, the original certificate will never be logged. However, if you reissue the certificate and allow it to be logged, the reissued certificate will be logged. Additionally, all reissued certificates going forward will be logged, unless you specifically choose to have that reissued certificate kept out.
To get a duplicate certificate with a different CT logging setting, reissue the certificate and change the CT logging setting on the reissue certificate form.
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