You said that old and new were both "domain123.com", so you shouldn't need to do anything as the HTTPS should just change to the new certificate when needed.
If you really went from domain123.com to domain789.com, then you need to take more action. No matter what else you do, you need to update the External URL (Server Document - Lotus Traveler tab or NTS parameter override) to use the domain789 address. This will cause any new links (such as the profile) to use the new one instead.
If it is an option, you should map (in the network, not an HTTP 302 redirect) domain123 to domain789 which should cause the devices to have to change nothing. Any new devices will be configured with the new External URL and over time will all end up on domain789.
If mapping isn't an option, you will have to reconfigure all the devices as you did when they were brand new. Assuming the external URL is correct, they should all be on domain789 then.
Traveler & Domain (Server) Change -... (Michael Sloan 5.Jul.12)
Feedback response number RSSN8VWRPL created by Robert S Sielken on 07/05/2012
. . RE: Traveler & Domain (Server) Chan... (Robert S Sielke... 5.Jul.12)
. . . . RE: Traveler & Domain (Server) Chan... (Michael Sloan 5.Jul.12)
. . . . . . RE: Traveler & Domain (Server) Chan... (Robert S Sielke... 6.Jul.12)