You have multiple Domino Domains and you want to do a free/busy lookups across them all for Exchange users. as well as existing Notes users.
This would come about if there was multiple Domino organizations merging or the lack of Directory Assistance in the existing environment.
To resolve this issueFirstly you need to be using the latest build, 188.8.131.52 onwards.
Set up Directory Assistance [DA] in Domino if not already setup
In CMN, set the Domino server to the one running DA, normally a hub server.
Secondly you need to have a Certificate for each autodiscover.domain.com
You need to make sure all the DNS entries have been created.
Add the availability namespace for each domain in power-shell
Create users and contacts with proper SMTP addresses.
There is no need to change or add the set-cmnautodiscoverconfig from the initial primary domain.