Except for AAR, TA, and convertibles, big block clones tend to command more $$, if done well in none original combos, than equivilent small blocks. We aren't comparing original big blocks to cloned big blocks, we're talking about a 340 auto with no engine, wants to make it a 440 manual. I think it will increase the value. Obviously if it is a tossed together carelessly and finished with a green vinyl top and gold exterior, it becomes a sales leper. But paint in blue, black, or red, do up the rest of the car to look original, it will be worth more to most, not all buyers, except those specifically looking for originality.
I think we've all seen guys loose their mind and pay stupid prices for original stuff, whether complete cars or date coded parts.