Remove a domain

We are running MIAB v60.1 on Ubuntu 22.04.1 and have 3 domains

One of the domains has only one user and after archiving that user
it is still showing the domain belonging to the archived user in SYSTEM / STATUS CHECK

Is there a way to totally remove a domain and all it’s users / files from the server ?

You have either missed a alias or a Custom DNS setting for that domain. Once all users, aliases, and custom DNS settings are removed, the domain should be removed as well.