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Howdy,
Hmm, can you say a few words about your setup? Here's a few questions --
Which distro/version are you using?
When you installed Virtualmin, did you use the install.sh script?
The domains you currently have setup in Apache, were they all added via Virtualmin ?
Also, regarding the second error you mentioned about it not being able to enable the SSL feature, you can only enable one SSL site per IP address, unless your SSL certificate is setup as a wildcard certificate.
-Eric
I also have this issue. I enabled letsencrypt on all domains, even though I don't have a wildcard cert. I tried migrating these domains to a new virtualmin, and some domains failed with this error message, and mysql and logs were not migrated as the script stopped at this error.