As per post over here:
and here:
I needed to change my primary/default domain as renewal fee has gone up, so I did it (MIAB@v0.48).
I forgot to change the rDNS/PTR record, but it was quick fix.
The dashboard is showing everything is OK.
But I have just found that none of my other domains are now working (are not accessible from internet) and e-mail are not being delivered either 
The new primary/default domain web/email works fine.
Anyone any ideas?
Where is your DNS for the other domains being served?
If on the MiaB you need to change the name servers at the domain registrar. If externally, you need to change the MX records with the DNS provider.
DNS is served by my MIAB.
and I have changed GLUE/Nameserver(DNS) before hand to avoid any problems on the new domain.
I do not think that the primary/default domain would work otherwise??
I have tried the DNS script
~/mailinabox/management/dns_update.py
But no change.
I have to step out for a few hours (I am already late) so I can’t do anything now, but if you’d PM me with your MiaB hostname and at least a few of the domains (if not all) I can look later when I return in 4-5 hours.
Did any of the domains have DNSSEC enabled?
I have run the setup script again
sudo mailinabox
Primary Hostname: box.main.domain
Public IP Address: 111.222.222.111
Public IPv6 Address: 2a01:…
Mail-in-a-Box Version: v0.50
Updating system packages…
Installing system packages…
Initializing system random number generator…
Firewall is active and enabled on system startup
Installing nsd (DNS server)…
Installing Postfix (SMTP server)…
Installing Dovecot (IMAP server)…
Installing OpenDKIM/OpenDMARC…
Installing SpamAssassin…
bayes: synced databases from journal in 0 seconds: 44 unique entries (44 total entries)
Installing Nginx (web server)…
Installing Roundcube (webmail)…
Installing Nextcloud (contacts/calendar)…
Nextcloud is already latest version
Installing Z-Push (Exchange/ActiveSync server)…
Installing Mail-in-a-Box system management daemon…
Installing Munin (system monitoring)…
updated DNS: main.domain,second.co.uk,third.co,fourth.uk,fifth.wiki,sixth.uk
Your Mail-in-a-Box is running.
So lets see if anything changes in 48 hours …
Nope, the NEW primary/default domain at point when I start changing over did not have DNSSEC enabled.
I have “DNSSEC ‘DS’ record is set correctly at registrar.” in the control panel as well for the NEW primary/default domain.
Finally I have cracked it.
So I have successfully managed to change primary/default domain name
and sub-domain name as well:
box.domain.win —> mail.mymail.com
here is what I have done:
1] change you rDNS/PTR record at your VPS/ISP provider
box.domain.win —> mail.mymail.com
2] change the External nameservers for all [other] domains at your Domain Registrars
ns1.box.domain.win —> ns1.mail.mymail.com
ns2.box.domain.win —> ns2.mail.mymail.com
3] change your Ubuntu Server “host” name and reboot
box.domain.win —> mail.mymail.com
4] run the “sudo mailinabox” and change the primary/default domain name on the BOX
5] change the DNSSEC details as requited on all [other] domains at your Domain Registrars according to details from " System Status Checks" page.
6] change all the “Aliases” e-mail addresses for [hostmaster@, postmaster@, admin@ and abuse@] so they point to correct/new primary/default domain
I have been without e-mails for more than a week (as per my other post about OVH), but it should only be no more than 48h and those e-mail will be re-delivered if you have a decent Domain Registrar 
When you changed the hostname, did the DNSSEC DS records change for what was the original primary domain?