Wouldn't PNCL management try to seat-lock 9E pilots into their respective a/c, and also seat-lock Colgan pilots into whatever a/c they're currently on? I would think if the seniority lists were merged that mgmt would setup something like Republic/Chataq/Shuttle, where you've got one seniority list, but you're hired onto a certificate and seat-locked for 2 years due to costs of retraining lateral a/c transfers.
Evidence=ATL flying at 9E with the 2 yr seat lock for pilots transferring/assigned to that base.