Do I need a separate project for users in a subdomain?

As long as all of the users are in the same environment, every one of them can be migrated using the same project.

As long as the administrator has access to all of the Active Directory objects, the same administrator account can be used.

The primary reason for splitting items between projects is to stay organized.

Note: In an Office 365 to Office 365 migration, we recommend splitting the projects due to the project-wide Recipient Mapping support required by the guide. In this scenario, you would add one set of users of one sub-domain into a new project and repeat for every added sub-domain. For each of those projects you would add the respective Recipient Mapping Support Option. 

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