Migration from Microsoft Entra Connect Sync to Entra Cloud Sync

hi Ivane99​  here are few recommendation you should try -  yes, what you’re observing is a known behavior when running Microsoft Entra Connect Sync and Cloud Sync in parallel for different organizational units (OUs). Each synchronization method maintains its own connector space and object anchoring, so dependencies (like group memberships or user-linking between sync types) aren’t shared across the two sync engines.

In your case, since users are synced by Entra Connect Sync and mail groups by Cloud Sync, the Cloud Sync agent doesn’t have visibility into the user objects managed by Connect Sync — which is why it can’t process group memberships or update Entra ID accordingly.

A few recommendations to help you move forward:

Plan a full cutover per OU type (users, groups, etc.)

Avoid splitting dependent OUs between the two sync methods. When possible, migrate all related objects (users, groups, and memberships) together under a single synchronization type — ideally Cloud Sync if that’s your long-term goal.

Use staged migration

You can follow Microsoft’s documented staged approach to transition from Entra Connect to Cloud Sync. It allows gradual migration by disabling sync on the Connect side once the Cloud Sync agent fully manages that OU.

Plan a migration to Microsoft Entra Cloud Sync

Verify attribute flows

Ensure attributes like memberOf and objectGUID are correctly populated and that your Cloud Sync agent is configured with the proper scope filters and join rules.

Licensing and group-based access

Since you’re using dynamic or license assignment groups, confirm those group memberships resolve correctly once objects are fully synced by the same engine.

You don’t necessarily need to sync all OUs at once, but for objects that depend on each other (like users and groups), they should be moved together to the same sync method to maintain relationship integrity.

Hope that clarifies the behavior — you’re definitely on the right track, and once all dependent OUs are migrated to Cloud Sync, the issue should resolve itself.