I would think the existing problems will still be in the new engine replacement. These engines are all built at the same time and a certain amount are set aside as replacements as per some Six Sigma curve. Once a problem is discovered, these engines would not be sent back for a retro fix as it would be an additional cost that the company is not willing to cover. Imagine what the cost of the replacement engine would cost if they did. All that happens is the crated motor is shipped to the dealer to replace the damaged one and hopefully it may or may not have the same issue. If it does it would be outside the warranty period.
I had a choice of either a new crated motor or getting the one I have rebuilt (too much oil by PO) when I bought the car. I sent it out to be rebuilt and the shop uses the latest improved parts. This will ensure that existing issues are delt with with the latest upgrades. In my case there is a substantial savings between rebuilt VS crated factory (can you say $6,000 CDN
). Most industries behave in the same manner, cheaper to NOT recall the motor and rebuild it.