Windchill server rename and move to another Windows domain

Within our organization we are migrating everything into a new domain. We use an automated tool but that does not support Windchill.
I have one server Running Windchill on Apache, I did some checks and find loads of files with entries to the “current” name and domain. Is there an easy way to get Windchill working after the migration or do I need to update all files manually?
Tips and advice are more than welcome