Virtualmin dns server rebuild all. > Virtualmin Guide

Do you have this issue with all your domains? Well, you can use the command line API to turn off and on the BIND feature on all your domains like so:

virtualmin disable-feature --dns --all-domains
virtualmin enable-feature --dns --all-domains

This should recreate all zones for your domains. If you still have missing A records then, let me know. I'd need to take a look at your templates and config then myself, for which I'd need root access to your Virtualmin and SSH shell.