Just came here to link this with this thread..
I had the same issue, bcs I seem to have manually edited /etc/postfix/main.cf
So yunohost tools regen-conf -n -d returned:
...
-virtual_mailbox_domains = ldap:/etc/postfix/ldap-domains.cf
+virtual_mailbox_domains = /etc/postfix/virtual-mailbox-domains
...
I changed that manually and it is up and running again.