If you change an engine...there are many different steps. Sometimes if you are just chuking out the old engine and putting in the same engine but a newer one then no need to change the gears and suspension...sometimes when you put a newer model engine in an old car you need to change the gears and suspension as well.
When converting from petrol to diesel you need to change ..engine, gears, suspension, radiator plus numerous other small things.
As for the change of engine number in registeration book, that a relatively cheap process, I cant remember now exactly for how much but I think it used to be just Rs. 500 to 1000.