Merging of seniority lists is never an easy task. I am familiar with 3 instances of mergers/acquisitions/bankruptcies and in each instance the redefined seniority list was a disaster.
It usually comes down to negotiations between the respective unions and it is fair to say that those pilots directly involved in the negotiations will look after their best interests first, and then the interests of their fellow union members. If a consensus cannot be reached, then arbitration follows.
Needless to say, your relative prior seniority plays a role but it is not the only factor. For example, what types of aircraft are being utilized at the new airline? Does being a Captain before these events mean you will still be a Captain? How long was your airline in operation as compared to the other airline? Who bought who? Which airline was the successful airline and which one was headed for the recycling bin?
There is no easy answer and I can guarantee that some pilots will benefit while others suffer. It usually leads to hard-feelings amongst some and that is understandable.
Unfortunately, pilots are their own worst enemies in these regards. The company doesn't care one bit, provided there are no added training costs associated with the merged seniority list. Seniority of pilots is rarely a issue for management leading up to a merger.
The !!!!e only hits the fan after the bigwigs have made the merger a done deal. They know full well that the respective pilots will battle it out. If it gets too ugly, an arbitrator who usually has no frickin concept of the importance of seniority, will make the decision.
If you are about to undergo the merging of your seniority list with another airline, then fully expect to view the results as baffling. I would be extremely surprised if things went smoothly and the majority of pilots were happy in the end. Hope it works out for you though.