If the original CoC was issued by one electrician and validated by another it's highly unlikely both electricians missed the fact there was no main earth. I'd assume, as Dave suggests, it was lost at some stage.
What earthing arrangement was the installation stated as having on the CoC? Do you know what earthing arrangement the supply authority actually provided before it went missing? There are some earthing arrangements that are the sole responsibility of the property owner such as 'TT earthing'.
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