That's complicated...the merged entity would have to honor ALL existing obligations on both sides. That includes the CHQ contract and the CAL scope clause.
They would most likely have to negotiate with one party or the other and make a deal...ie buy out CHQ's contract and park (or re-assign) the e-jets or give concessions to CAL-ALPA in exchange for keeping the existing e-jets, but not allow any new e-jets.
Another factor is how the UAL/CAL integration occurs. I'm sure they will keep the UAL name and certificate, and over time move CAL planes and pilots onto that. This will require essentially a new contract covering all AUL and CAL pilots...presumably during the negotiation phase they would work something out.
But until they actually merge certificates and seniority lists (which could take years, see exhibit #1: US Airways), the e-jets could continue to fly for UAL.