Trans-system medication involving modern and Ayurvedic agents is always a problem. There is scientific data on the interaction between thyroxine (Thyronorm) and at least 40 other medicines ranging from antacids to calcium carbonate to antidepressants. However there is no data on interaction with non-allopathic agents.
One has to keep in mind that there is strong possibility of interaction because many allopathics medicines are indeed extracted from plants such as quinine, digitalis etc.
It is because of these problems that in 1996, Supreme Court had prohibited allopathic doctors from prescribing agents belonging to other systems.