Why are Cloud-based users removed unexpectedly during re-initialisation of the Configuration Data replication group?

I’ve installed the Microsoft Intune Connector role on my ConfigMgr 2012 R2 SP1 Site Server. But I’ve noticed that my cloud-based users are removed unexpectedly during the re-initialisation of the Configuration Data replication group (whether it occurs through the Replication Control Monitor (RCM), component or manually by using the Replication Link Analyzer tool).

As a result new policies and applications cannot be sent to users, and existing policies are removed.

The weird thing is the users are added back to the Site Database after the next successful synchronisation with the Intune service and everything works as it should.

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