You can apply for the subsequent rounds of counselling as long as the procedure goes on. The mop up round of counselling in states for MBBS or BDS seats is only conducted if there are vacancies.

If so, you can apply for the mop up round in the state counselling. However, the rules are different for different states. For some states you need a fresh registration, while in others you only need to apply for up gradation (without registering again).