Alright so here is a more legit reply. I would guess before the explosion, when turning all of the people in to blobs this only effected the scientist. When he beg to die this explosion could have been two things. Number one, the explosion only killed the others and not the test subjects including the daughter? Number two, This was not an explosion just like a force field or a shield of energy just flew out of him with he spilt!
Then here is another idea. If his daughter died in a explosion, the pendant could have been left behind, the others who were also freed the could have found this.
My last idea is connected to the others (test subjects) being freed is when the scientist found Hakuoro and Mikoto, and when they took the baby the pendant fell off. And the others found this pendant.
It's been quite a while since I've played the Visual Novel so I can't accurately remember this but considering what we were told we can accurately assume two things. 1) Mikoto and the daughter are both "dead" as in they were dissected and are not alive now and 2) There are a lot of these animal beings based on the scientists stating they can create many of the same "Mikoto" if that is what Hakuoro's preference was.
From this we can draw the conclusion that Eruru is actually unrelated completely to Mikoto in that she isn't her descendant. However it is completely plausible and most likely that when all of the Animal people escaped after the scientists turned into blobs that there were already clones or animal people who resembled or were clones of Mikoto. In that they were either already made clones of her or that Mikoto (being based on a test number name) was most likely a series of products manufactured by humans and therefore there were many "mikotos" already.
And by this it is quite easy that, after a long while, you have Eruru resembling her because she is probably a descendant of one of the other animal people who looked like "mikoto." As for the pendant, i would say it is just a coincidence that some people found it and after a long while it made it's way to be Eruru's hair piece because logic.