This is expected functionality.
The Merge Rule expected behaviour is described in the Active Roles Synchronization Service Administrator Guide as follows:
A merge sync rule allows you to merge attribute values between the source and the target data system. As a result these values become identical.
Since a CSV file is treated as a read-only system and is never updated, normal behaviour for a Merge Sync Rule is not possible and the behaviour of a Forward Sync Rule is used instead.
WORKAROUND
None.
STATUS
Enhancement Request 779224 has been created to change the existing behaviour of the Active Roles Synchronization Service and hide the option to create a Merge Sync Rule when working with a CSV data source. This will reduce confusion when working with CSV files.
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