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Hello,
There are different counselling process of All India quota seats and state quota seats. The counselling for Deemed Universities is held through All India counselling. So to apply for deemed university college you have to register yourself for All India counselling.
But to get admission in medical colleges of your domicile state you need to apply for state quota counselling. There is no upgradation process. As both are two separate process. You can apply for both simultaneously.
Also if you get allotted in first round of any of the counselling then also also you can apply for their second rounds too.
Hope you get some clarification.
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