Just because they were living together in the past doesn't mean the calls were the same. It's speculation. The business about genes is a red herring. Are you suggesting you can tell what kind of mating call they had in the past, based on DNA?
If I understand what you are trying to say, you feel that all females in the previous single population responded to more than one call. If the females in one of the two populations only respond to one specific call, while females in the other group only respond to the other call, gene flow is disrupted and they are confirmed as two different species.
However, mating calls are very specific and generally tell a female which male belongs to her group and will not respond to other calls. Unless these particular frogs are an anomaly in this respect we conclude they had only one call. However, the number of initial calls is not relevant to speciation, the response or non-response to a call determines whether gene flow is disrupted.
DNA can not tell whether they had a single call or not, but that is not what I said. DNA will tell us if they in fact were a single intra-breeding population and mDNA will tell us when they separated. The thing about the genes was not a red herring, you simply didn't understand the significance of the mention of them.