I haven't done this procedure in a while, but if I recall, changing the domain has the following effect:
rnolabise02/admin#configure t
Entering configuration mode terminal
rnolabise02/admin(config)#ip domain-name newdomain.local
% Warning: Updating the domain name will cause any certificate using the old
% domain name to become invalid. Therefore, a new self-signed
% certificate using the new domain name will be generated now for
% use with HTTPs/EAP. If CA-signed certs were used on this node,
% please import them with the correct domain name. If Internal-CA
% signed certs are being used, please regenerate ISE Root CA certificate.
% In addition, if this ISE node will be joining a new Active Directory
% domain, please leave your current Active Directory domain before
% proceeding.
% Changing the IP domain-name will cause ise services to restart
Proceed? [yes,no]
If you don't need the self-signed certs for anything, then you can ignore the message above about certificate re-generation.
And you'd need to do this on every node. One at a time, waiting for services to restart.
Ensure that the nodes are all still registered to one another during this process - that's the part I would test in the lab (unless someone can confirm). From memory, I think I de-registered all the nodes, did the domain name change on each one, created new Admin certs for all, and then registered them all back again. A lot of work, but it felt like the right thing to do. And it succeeded.
