By Matt Shadbolt | Senior Service Engineer | https://blogs.technet.microsoft.com/ConfigMgrDogs/
Important: This guide is intended to explain how a migration blocker occurs, and how to remove the blocking issue. The guide is not intended to provide guidance on how to redesign your grouping/targeting to achieve functionality caused by the blocking issues.
We suggest you thoroughly review your grouping/targeting strategy before making any changes.
One of the options for group criteria in Intune Silverlight is to query based on the user’s Manager in Active Directory. It was never a popular feature so we stopped supporting it a long time ago. If you still have any groups that you’ve got configured to use this membership criteria, you need to remove it, or the groups that use it, or it will block your migration. Here’s how:
1. Login to https://manage.microsoft.com with your Admin credentials.
2. Browse to the Groups tab.
3. Select each individual group, and expand out the Membership Criteria. You’re looking for any group that contains Manager as the criteria.
4. If you’re actively using this group for targeting/reporting/etc, you will want to create a Direct Membership based on the group membership. Do this by selecting all the members of the group and clicking Create group from selection. You can then redeploy all the apps, terms and conditions, and policies to this new group.
5. If you’re not using the group or Manager criteria, right-click the group and click Edit.
6. In the Criteria Membership tab, you can see Include members with these managers. Click Browse.
7. Select the name under Selected managers, click Remove, and then click OK.
8. You need to perform this procedure for any Intune group that has any membership criteria using the users’ managers.
Your migration should now be unblocked for this issue. For more information about configurations that can block your Intune migration, see http://aka.ms/intunemigrationblockers.