In SERVER-43860, we fixed the behaviour of $merge in the case where we have {whenMatched: pipeline} and {whenNotMatched: insert}. For upgrade/downgrade purposes, we made this new behaviour conditional on the presence of a flag, useNewUpsert, which is set by 4.4 mongoS on aggregations that are sent to the shards. We then backported this fix to 4.2.2.

However, in cases where a $merge is sent to a shard as part of a $mergeCursors pipeline, the 'useNewUpsert' flag is not set on the command. In these scenarios, the old incorrect behaviour is still observed.