How to keep term relationship to node, when term changes vocabulary in Drupal 7?

I've inherited a site with a very big hierarchical taxonomy:

Vocabulary name: categories
--term: company name
---- many child terms
-- term: country
---- many child terms
-- term: issue
---- many child terms

I realized it would be easier to create Search facets and Views with appropriate content if I set up each of these parent terms

company
country
issue

as their own Vocabularies.

I created the new Vocabularies and used Taxonomy Manager to shift all the sub-terms to their new vocabularies.

I then updated the Article node content type to be associated with the vocabularies

company
country
issue

Unfortunately I also noticed the sub-term relationship between the Article nodes (all 4,000 of them) and the Terms was now lost in the display.

I've been searching for a way to update the vocabulary references for the Article nodes, but I'm still not sure - even after looking at the taxonomy module in Drupal 7 - how the vocabulary is associated with the node. I see new field_data_field_machine-name tables are created for each new Vocabulary - and that this is where the termID and node/entity ID as assocaited.. but where does the node/vocabulary relationship get established? And how can I updated the Vocabulary for a node automatically when I move a term from one vocabulary to another?

I also haven't found this exact questions in the many forums I've been looking in. I wasn't sure if this question was related? http://groups.drupal.org/node/214928. I've recently move this site from Drupal 6 to 7 so it doesn't help that there are a lot of dead tables from D6 cluttering up the database.

So I just would like to know if it's possible to simply do what I want to do?

thank you.