It appears that the collectionUpdate mutation doesn’t accept metafields. Is there a reason why? It seems odd, because the productUpdate mutation does accept metafields (along with others like customerUpdate and draftOrderCreate).
In the meantime I can use the REST API to update metafields, but it would be great to be able to use the GraphQL API to reduce HTTP requests and keep my code clean.
Just wanted to update you to let you know that this has now been fixed for the API release candidate version for development, and will be included in the upcoming stable version 2019-07 for production.