Try this:

1. be sure you have 'Taxonomy wrapper settings' ENABLED in admin>>settings>>category
2. list categories of one of your containers (admin/category/x) and click on the 'bulk edit' tab.
3. choose one or more of your categories using the checkboxes, and go to next step
4. select 'Container' and 'Parent' and go to next step
5. make your edits, go to next step and confirm

Now:

Categories are updated, but Terms in the Taxonomy tables (term_data table, and eventually others) are NOT.

Filed this as a critical bug, as "many taxonomy-dependent modules directly access the taxonomy database tables, instead of using the taxonomy function interface."