This problem has had me stumped several times over the past few years, but I think I finally figured it out. With many of our domains, we have the address "postmaster" set up as an alias to the system-wide postmaster. So, there is a virtual domain mapping with postmaster@domain.com defined as postmaster. Then, in /etc/aliases, there is a system-wide alias for postmaster, pointing to another address.
The problem is that, whenever a domain owner deletes this alias in their domain, or whenever we delete an entire domain (which includes deleting this alias), Virtualmin not only deletes the virtual domain alias, but it also deletes the system-wide postmaster alias too! After a while, we eventually discover that we are no longer receiving mail addressed to postmaster, and we re-add it back to the aliases file.
There needs to be a way to prevent domain owners from deleting system-wide aliases like this. They should only be able to delete aliases which they created, or which are explicitly assigned only to their domain.