Yes, you can give the two flats on rent and claim deduction in respect of interest paid in respect of the home loans on the two flats in your return of income.
If the property is acquired from your self earned income, then you can obtain an injunction from a civil court restraining your father etc., from dealing with your property or your share therein. If the property is acquired by the father from his income, then you cannot prevent him from dealing with the same.