We created a multi tenant application on Azure. In order complete the configuration, we created an Active Directory per location. We want to use directory sync with password sync as we have on premise Active Directories. When we ran the Active Directory sync tool with our central office, the user data got properly migrated using the custom domain name we created for that office (i.e. all user accounts end with @mycustomdomain1.com). After that, we started doing the same synchronization process with the second office. However, when we did this, the users got migrated to Azure with the Microsoft default domain (i.e. @xwz.onmicrosoft.com) instead of to the custom domain we created for that office (i.e. @mycustomdomain2.com). I am really confused and would like to know how to get this fixed.
There are no differences in the domain configuration we did for the two directories and domains above: All the custom domain verifications were passed on Azure and all the custom domains are set as primary. Why the users get migrated with the Microsoft domain instead?