You might be able to trick Virtualmin into doing it by changing some options in the Website options for the virtual server. I’m not sure that’ll do it though.
I’ll ask Jamie to chime in. But I’m thinking you’re going to wish you were keeping regular backups (we all make mistakes…it’s having backups that makes all the difference in how painful those mistakes are). Webmin and Virtualmin both have great backup facilities built right in.
One thing that you could have done if you’d had no backups is to disable the website feature for all your domains, and then enable it again. This should tell Virtualmin to re-generate all the Apache config entries, although any domain-specific customizations to the configs would be lost.
I was going to suggest that too but didn’t know if it would delte the home directories, this is a good thing to know. I typically do that with DNS when I move domains around. It will then update all the slaves and the coding will be cohesive (providing you’re not doing any custom coding