Hi @sonill
Our plugin is largely backend based and works to switch the taxonomy value listed in the appropriate database tables from Taxonomy A to Taxonomy B. However, I can’t recall it ever being formally tested with WPML. That said, if the original terms and translated terms are all still within the same taxonomy, I think it should work just fine, and not break the associations.
If you have a test install to work with, it’d be worth trying and testing there first.