We have discussion about Late Chalcolithic period (4500-3600bc) in Armenia. Here an old thread.
Given that the LC period samples from Areni have brides from North we can't see what was the main population living in Armenia in that period. But fortunately we have one Leyla Tepe period sample from SE Azerbaijan.
Here it's closest population.
Distance to: AZE_Caucasus_lowlands_LC
Now compare it to preceding Neolithic period.
Distance to: AZE_Caucasus_lowlands_LN
The shift to South in Late Chalcolithic is obvious. This is consistent with archaeologic records that in that period there was a influence from North Mesopotamia. Which introduced Chaff face ware instead of gritstone tempered ware. Also rectangular houses instead of round houses. Jar burials were another feature of this culture.
It must be noted that those Mesopotamian influences are not surprising. In 5th millennia BC it was the culmination of Ubaid culture that started to have influences to all neighbours. For example in Syunik LC Godedzor we have pottery made in Ubaid manner. This offcourse do not mean a direct migration from Mesopotamia like some Georgian scholars who suggested "the so called Uruk people" . But definitely a cultural influence occured.
As for Areni. We still don't know why they have an admixture from North. But it's also visible in archaeology. The occasional presence of shell tempered ware in that cave points to contacts with regions in North. Maybe it was a just trade contact. Maybe something more serious. It must be noted that none of Y dna found there is from North. Only the women MitoDNA.