What should be done with the balance sesame seeds after tharpanam? Can we store and reuse it again? Some say the balance seed should not be used and it should be added to the bhugnam.

No, the balance sesame seeds should not be retained. Tharpana prayogam instructs on what to do with the remaining seeds and darbha grass; there is a sloka that has to be chanted for the balance seeds and darbham; one has to chant the sloka and offer the balance sesame seeds and darbham accordingly.