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So, my understanding of the contamination effect sidequest is this:
Luke and Asch are different from other replicas in that they are a perfect isofon- that is to say, they are identical replicas with the exact same 'fonon frequency', which is akin to this world's version of DNA mixed with magic energy. Normal replicas are physically identical but fononically (to make up a word) different; they have a different energetic frequency.
In experiments involve perfect isofons, the examples of which being Luke/Asch and the cheagles imprisoned in Ortion Cavern, there is a staple pattern:
1) once the replica is made, at some point, the original dies because of phonon separation and physical degradation because magic science.
2) The replica then undergoes a process of fusion with the fonons from the original, after which the original's consciousness awakens in the replica's body.
Other interpretations of this could be that the cheagles experienced a fusion of consciousness upon the re-fusion process that the game refers to as the 'big bang'. Because the perfect isofons share memories upon re-fusion, one cheagles' experience of its replica's death could be singular; they each experience each other's impressions of the event and thus occupy both positions in their memory. After all, as one entity, there isn't room for anything else.
Now, the expectation is that that the original will die first, and then reawaken inside the replica's body as a result of a fusion process. So in a sense, the replica consciousness is destroyed, with its memories and emotional impressions inherited by the original.
This doesn't seem to be what happens with Asch and Luke simply because upon Asch's physical death near the end of Eldrant, he becomes the subordinate personality when fusing with Luke. We don't know, however, whether this is what really happened. It could be that Asch's will, as it were, simply persists within Luke for long enough to lend him power to defeat Van before finally experiencing the big bang proper once he's released Lorelei and his corpse is safely nestled in his arms... If that's the case, we come again to the big question, who is it that returns at the end?
The originals in the cheagle research presumably died of natural causes; simple fonon separation causing an organic big bang process with their nearby replicas. In Asch's case, he dies a violent physical death a good deal away from his replica. Luke, who seems to be undergoing a fonon degradation of his own as a result of the Tower of Rem incident, doesn't (immediately, at least) send Asch his life essence in response as per the normal perfect isofon replication process. Instead, the reverse happens, and it seems Asch then becomes subordinate within Luke's consciousness. Jade mentions wanting to be wrong about his research about perfect isofons during the sidequest bit, and the norm in these instances is the opposite of what seems to occur. Compound this with the personalization of the whole 'promise' bit at the end with Tear and it seems pretty likely that the figure at the game's end is Luke and Asch reformed into a single consciousness bearing both memories, but with a stronger attachment to the replica memories.
Unfortunately, he'll still probably have to marry Natalia because of the royal edict. Even though Tear is so much lovelier...:(