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Found the answer. (It's in the SQL Data Comparison SDK samples, which I couldn't actually find a working link to. I had to find the SQL Comparison SDK samples link, and change the URL!)
tableMapping.MatchingMappings.Clear();
tableMapping.MatchingMappings.Add(mapping.FieldMappings["FieldName"]);
tableMapping.RefreshMappingStatus();
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I'm not seeing anything relevant, but hopefully I'm just missing something.