DocumentTypeId not updating with taxonomy updates

I had to reorganize the taxonomy with new groups and categories. Looking at the taxonomy.json, everything is updated except for the DocumentTypeId – the group and category in this are still the old version – OldGroup.OldCategory.DocumentType. In the past, I have manually overwritten with the updated names in taxonomy.json, but that breaks the classifier and extractor, which I cannot afford to do at this point. Is there a way I can get taxonomy.json in sync with the Taxonomy Manager without breaking what I have built already?