I’m not a fan of sibling-swapping, but it’s not exactly the same here. Mia has memories of two lives now, and she had something with Connor in one and in another got engaged to JJ (a JJ who wasn’t a murderer, though he could become one again, depending on how they decide to handle him if there’s a spinoff, which is unclear since Arrow’s not the best at doppelgängers, which this situation is at least similar to, though not the same as). It’s messy, yes. Do I trust these writers to not make it ultimately be sibling-swapping and even reveal that Mia and Connor maybe had something at some point before she was with JJ? No.
Really, it probably all depends on what they do with JJ now that he has both sets of memories. And like I said, I wouldn’t be surprised if they decide to have him completely change back to murderous JJ — while continuing to stress how Laurel could and did change and is totally a hero now and have her continue to say that JJ can’t change.
Of course, we may never get these answers. It may not be ordered to series.