Microsoft has just updated the following KB Article:
Cloud User policy assignments are removed from Configuration Manager sites during data reinitialization
Symptoms
On a Configuration Manager Site server that has the Microsoft Intune Connector role installed, cloud-based users are removed unexpectedly during reinitialization of the Configuration Data replication group. This reinitialization may occur programmatically through the Replication Control Monitor (RCM) component, or it may occur manually by using the Replication Link Analyzer tool. The users are added back to the site database following the next successful synchronization with the Intune service. Before the next successful synchronization occurs, new policies and applications cannot be sent to users, and existing policies are removed.
Note This issue does not affect stand-alone sites.