as for resale, it can be. a few years used car with a changed engine means car was not taken care of. to attract customers you will have to reduce price. but for a old car, it is normal. and there will be no reduction in price as long as it works good.
for this you choose an engine and note engine no. then you go to police and check engine no against list of stolen engines. when you get clearance, you buy and install engine and go to excise and get it updated on reg. book.
also i have heard there are people that can etch your old engine's no on new engine. you can consider that too if you are in a big city.
mostly when you will go to sell a car, people will look at engine and say 'yeh to kabuli engine hai' it is very rare for a customer to check engine no.
it is good too obey the rules. otherwise nobody does that.