There seems to be a bug in /v2/orders/calculate regarding metadata in that it accepts metadata on line items but does not return metadata in the response. It does accept and return notes which seems to indicate that metadata is just missing, not intentionally accepted but not returned.
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Thanks for bringing this to our attention. The team is currently looking into this. 
I also am currently blocked by this limitation. We’re working around it by assuming that the reply from Calculate preserved the order of the line items in the request, but I’d VASTLY PREFER counting on metadata.
I’ll pass this on to the team.