You don’t need to delete them. They can be repaired, though I don’t remember how, off-hand…searching…here’s one thread about it: Domains Showing as Numbers - #15 by Ilia (Ilia provides a command that restores just the metadata, which is what’s missing that leads to numbers in place of a domain name, and probably all that’s missing, unless something catastrophic happened).
There have been a few threads about this problem. It can happen when there’s a disk error, out of disk space, or power outage , or reboot, or OOM killer killing Webmin, while the domains are being updated (maybe during a confiig check or something else).
An update would not cause it, unless Virtualmin’s postinstall tasks were running when one of the above problems occurred.