What's best a new engine w/different VIN or remanufacturing my engine? I would rather have a numbers matching bike. Or does that really matter very much regarding resell value later.
The next question I'll ask, if they are sending a new engine, will be ... Can I keep my old engine. Because new engines don't require a core to be sent in.
At this point I would take the new engine over the reman of the old - if that is what's happening - Your existing cases are potentially worn beyond economical repair, or any repair for that matter. As far as a "numbers matching" bike I personally wouldn't worry to much about it affecting resale.
If the dealer and the rep determined your engine is going to be replaced with new because it can't or shouldn't be repaired I think the factory can stamp the new engine with your VIN - which makes your question about keeping it mute because the old engine would have to go back to HD to get destroyed due to the VIN issue. But it seems like your deal with them is contingent on giving them the old engine as a "core exchange" regardless of whether they give you a new engine or reman the old one - otherwise why have you go through all the trouble (and expense) of putting all the stock parts back on.
Me, I would let them have the old boat anchor, because A) I don't have a boat, and B) I have enough projects around here to keep me busy..