Knowledgebase: SSL Technical FAQs
I get an intermittent server not found message when trying to access my site

If the web server is set to check the Certificate Revocation List, also known as a CRL, and the server is down, this can cause a time-out of the operation.
This will not be the certificates, but something related to the browser timing out on the operation.

See also:

What is a CRL?

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