Please show us the link that shows the agreement has been nullified since the merger. The agreement with JBI is a perfect fit for Rock Tenn, and their reasons for the merger to begin with.
In my experience, an acquisition is a risk to any projects that are underway. I've seen it happen several times that the acquirer says "freeze all projects" and proceeds to evaluate each one based over the course of the following months.
This could explain why the referral agreement doesn't appear(!) to have borne fruit yet... it may be going through a more rigorous review!
However, given the nature of the project (money savings / revenue generating) there really is no reason to believe RKT would kill it. I see the RKT acquisition of SSCC as more of an opportunity for P2O, than a threat. But it may well cause (have caused?) delays in the first site(s) getting started.