configsvr_commit_refine_collection_shard_key.js is doing a refresh in the shard in order to leave consistent metadata for the CheckShardFilteringMetadata hook, however, because there is no communication between the shard and the config server, the configOpTime is not being properly propagated, and if the refresh hits a secondary node that haven't replicated the metadata, we'll find inconsistencies when running the hook.

We could wait for the config server to fully replicate the changes before issuing the refresh.