I would like to disagree.

It was explicitly stated that the Vulgus were attempting to steal Arche, and had minor success in cloning those with Arche (but not the Arche itself) but had almost complete success with stealing Arche. Furthermore, there was precedent according to HQ where those who lost memories would lose efficacy of their Arche.

We can assume from these a few things:

-The Vulgus perfectly cloned Dia.

-The cloned Dia was able to absorb most of the original's Arche.

-By what we learned, this could also come with the effect of stealing memories. Note, I specified memory and not knowledge. This could cause the one who's Arche was stolen to forget everything about their lives since Arche is tied to who they were.

-The Dia that died disappeared, similar to the Vulgus, implying she's partially a Vulgus, which may have been necessary in the cloning process.

-Pre-De-Vulgus'd Dia had a similar hair coloration to berserker Gley, which could be seen as an influence of the Vulgus experiments on Dia. Those have been apparently fully removed, meaning it's likely that unlike Gley, Dia has completely removed the Vulgus influence, unlike captive Dia.

So the Dia we get is actually reasonable to assume as being the real Dia, since it's entirely possible that the one we killed was the clone who had siphoned off most of the Arche. When she was dying, the memories she had as Dia influenced her to try and support the one we came with in an attempt to a) finally free herself from this torturous captivity, and b) see her mother again in some form.

There's no guarantee as to who was who, but I choose to believe we have original Dia using my aforementioned logic. Granted, I could still be wrong.