abactae boves quaedam -- this is not abl. absolute: it's nominative and therefore the subject. Desiderantes is nominative and modifies abactae boves, and relictas [boves] (acc.) is the object of desiderantes.
Roughly: "Then, when some of the cows that had been driven away mooed, longing for those that were left behind [or just "the rest of them"], the cows that had been enclosed within the cave returned their call [vocem]. Having heard this [vocem is the antecedent of qua; literally, "this having been heard"], Hercules turned back."
Relatives in Latin can often best be translated into English as demonstratives, beginning a new sentence. In fact, in extended narrative, relatives, rather than demonstratives, are often used to connect one sentence with the next.