Toggling the featureCompatibilityVersion between 3.4 and 3.6 adds UUIDs to collections during upgrade and removes UUIDs from collections during downgrade. There are certain known bugs with operations such as mapReduce replace running concurrently with setFCV due to the way collections are created and dropped during mapReduce (see SERVER-36701). Workloads should be created for operations such as mapReduce and aggregation with $out that themselves create/drop collections running concurrently with non-trivial featureCompatibilityVersion toggling.