Yes. certbot --apche resp. certbot certonyl is both changing the Virtualhosts configuration. As visible from the above file, the new virtualhost config output by certbot can be misleading or even wrong maybe because of not correctly assembling the virtualhosts configuration. Deleting of certificates once i did by hand in the first time after i had revoked the certificates with certbot and i did accidentially not choose yes on the question whether to delete the folder, but i guess a revoked certificate and key would be of no use to be kept…