How to delete a domain from a certificate that is used for multiple sites using Lego?

Did you use the webroot method when you got your initial certs?

If so, is the webroot path the same in the HTTPS VirtualHost as it was in the HTTP VirtualHost? Maybe you just need to update the webroot path in your lego command?

Or, update the Apache VirtualHost so it does not redirect HTTP Challenge requests from HTTP to HTTPS. Maybe like this:

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