Consider, however, that each of the game lines pursues its own narrative style, with player characters being more heroic (and thus stronger) in some than others. Accordingly, there are for example two different sorts of Genestealer so far, one for Dark Heresy and one for Deathwatch.

Of course, you could still take an enemy from another line's book and then simply tweak its stats to better conform to your own game, gauging where combat would neither be too easy nor too difficult. For the product lines you mentioned, you should probably make opponents from Deathwatch somewhat easier, but enemies from Only War somewhat tougher.

Good luck!