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Oh, no!

To quote my reply: "The only reason to ever install manually is if you're using an OS that our installer doesn't support, or you're working on a system that is already in production." Sounds like you've got a system that was already in production....so, you can't use the install script on it, without it breaking things. There's a big warning saying don't run the install script if you've already got stuff configured on the system.

But, it doesn't harm user data. It just changes configuration files that can make things that were working before not work after (which is why we say in many places don't use the installer on a system that isn't a fresh system). So, it's not a big deal...we just need to configure that site and import it.

So, where is the site installed? Was in a user home directory? Was it initially created by Virtualmin or some manual configuration?

With that info we can proceed on importing it into Virtualmin and getting it re-enabled in Apache.

OK, so that's expected. When we configure Apache for use with Virtualmin we set it up for sites run out of /home. While it is possible to run sites out of /var/www and /home at the same time, there are some security implications (suexec can only work on one or the other, and with a Virtualmin install it is /home, so /var/www cannot also be suexec docroot), and some potential gotchas in how Apache resolves which site to serve that can be very confusing.

I would recommend you do the following:

1. Create new domain-based virtual hosts in Virtualmin. This will create a new directory in home named /home/domainname
2. Copy your files from your sites in /var/www into /home/domainname/public_html (if they are PHP apps...if CGI, they'd go in cgi-bin). Or, if it is an application supported by Virtualmin's Install Scripts interface (Magento is, since you're using Virtualmin Pro), you could start fresh and let Virtualmin install it...that way it could notify you of updates via email, make updates easier, etc. You could still import the database if you have data already in your old site(s).
3. If you copy the files over, rather than doing a fresh install with Install Scripts, you'd need to "chown -r domainname:domainname /home/domainname/public_html/*" to make it runnable under suexec as the domain user.

If you already have data you want to keep in the database, you can simply import it using the Edit Databases->Import Database tab. Or, if you want to dump and restore it into a new database, the Webmin MySQL module can be used. (Importing is done using the "Execute SQL" page.