Changing the colour of your car is definitely do-able and legal. You can go to the Excise Dept and ask them for the details just to be sure.
It is easier to register the new colour on the Registration Book if you are getting a new Registration Book issued, but it would also work on the old book (like the engine change) its marked down by hand in the centre pages of the Registration Book.
That being said, it is not something which is recommended - mainly because a colour change affects the genuineness of the car and hence the resale value goes down. We all know how a repainted car suffers a loss in value - a colour changed car suffers even more.
As suggested by others in the thread, you are better of getting a colour change through other more temporary means like car wrapping or plastidip. This way you can get the colour of your choice, without having to affect the car itself if you think of selling it.