HI Milan,
You said that the 500 users are already in Windchill because you are using an integration with Active Directory. If this was done correctly, then those 500 users should already be associated with an organization in Windchill. If it wasn't done correctly, then those 500 users are unaffiliated, and that will cause problems with more than just the migration.
Have you tried looking at the details for some of the users to see if they are affiliated with an organization?
Thanks,
Micah