The server was restarted automatically per the update schedule. This is something that your support should have considered before deleting the certificates. Your tool was (and still is) unable to generate new certificates for my site.
It’s completely reckless to delete certificates for an indefinite amount of time and simply assume that the server will not restart. If support wanted to delete the certificates, they should have explicitly informed me and restored the certificates immediately after when they realized it did not fix the issue.
Your support should not be leaving servers in a state where a simple restart can break them for extended periods of time. I think that alone says more than anything else I can leave in a review.