what is the best option to transfer property/ flat

Hi, I and my father jointly own a 3BHK flat in Pune, purchased back in 2007. But I alone have paid all the Home Loan EMIs and made it to nil. With my consent, my father has kept the house as mortgage in 2014 with ICICI bank, for a loan on it, for his resort business. EMIs of which are being paid by him. Now, I have asked him to- >> Payoff his business loan on our jointly owned house OR >> Transfer his business loan to his house/ business resort AND >> Make our jointly owned house, just on my name (as I have paid all Home Loan EMIs of it); by signing a Deed. Now here, I wish to know -- which Deed we should go for ? And how much will it cost ?