If you're using AD/LDAP, you can get it to synchronise on the Username rather than the Email, so as long as you aren't changing both of these you should be fine.
As for clients that aren't syncing with AD/LDAP, you can export your clients from the Client view, and do an Import and selecting a corresponding base sync to overwrite the current details that aren't changing.
There are a few other ways like running Queries on the database, or allowing the change to run through leaving the legacy domain behind with all the tickets.
Thank you for the quick reply.
We use OpenLDAP for authentication. We will have a look at your suggestion.
As far as I can remember we have never done a manual import. How long would this take?
Depends on the amount of data to import (don't separate the data, it's faster to do it all in bulk rather than parts), and the amount of activity on the help desk which will affect performance unless there's sufficient memory/RAM allocated to Web Help Desk.
Personally I've done some client imports with over tens of thousands of clients with appropriate data and the import only took a few minutes.
If you wanted to test this, you could create dummy clients with the same name and username with sequential numbering, and import them with hundreds or thousands of accounts.
Once done you can then search with the corresponding name or username, and bulk delete them all. - this way you can see how long it would approximately take when you get around to it.