Initial sync clones collections alphabetically. This means the "admin.system.roles" collection gets cloned after "admin.system.version" which holds the featureCompatibilityVersion document.

The "admin.system.roles" collection has a unique index on {role: 1, db: 1 }. In 4.4 we require all unique indexes to be upgraded to the latest format version. This normally happens as a part of upgrading the FCV to 4.2 using the command or when the index is first created. If an index is created before the FCV is initialized, then it will have an incorrect format version and cause 4.4 to fail to start up.

This affects 4.2 nodes that experience an initial sync and do not go through a restart before upgrading to 4.4. Repro coming soon.

Workaround: Due to the work done in SERVER-45374, restarting an affected node with at least a 4.2.4 binary will self-correct the problem.