Usually, when loaning Latin words, Russian uses the accusative forms of the Latin nouns and adjectives, and replaces the Latin endings with the Russian ones. There are numerous exceptions to this rule, but for the most part, it works.

According to this rule, the "correct" form is *референтный*, which is indeed the only form that was in use before mid-80s.

That said, many Russian publications in the 90s and after that, just calqued or even borrowed English "reference center", which gave *референсный центр* and *референс-центр*, respectively.

I don't think there is a lot of difference between the two, but *референтный* is both older and more aligned with Russian scientific traditions.