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.
CC is granted in some parts of the Country once for Entire Work, But in Mumbai the CC is first Granted up tp Plinth or Top of Stilt as the Plinth Size and Open Spaces are checked at this Stage before Granting Full CC for entire work as approved.
It is not always practically possible to obtain full CC at one go. There are huge premiums that need to be paid. If they are paid in one go, developer will incur heavy finance charges on the same, which ultimately will be passed to the consumer.