1. You will become the 100% Title-Owner of the Flat, after having Mothers 50% share transferred in your name, based on the Court order.
2. As per Stamp Act of MH State, ANY registered Deed (Sale /Gift /Release /.... ) requires payment of Stamp Duty, for the purposes of legitimate conveyance to the new owner (i.e. your sister).
3. HOWEVER, you can include your Sisters name in the Conveyance Deed (though not advised) by Gifting her only 1% in the said Property and paying Stamp Duty on value of 1%. This will be negligible and the most cheapest and legitimate for all purposes.
Keep Smiling .... Hemant Agarwal