We are going through this (albeit on a much smaller scale) with Frontier and Midwest. italgreco is correct in that the admin positions were all consolidated. Midwest no longer has a headquarters and many of Frontier's positions are also being moved to Republic in IND. Most positions involving customer contact and operations have remained, except for the few outstations in markets that were closed.
The absolute worst part is merging the computer systems. We still have to jump back and forth between YX and F9 systems...which isn't too bad except for our DEN-MKE flights, which both systems have flights on, and we frequently have to move non-revs back and forth between the systems.
Add in the code share complexities and it can get bad (like around spring break this year when the F9 systems weren't pulling seats out of inventory for YX flights and our Airbus 136-seaters were overbooked by 40 people!
But there are always growing and merging pains, and this too shall pass. :-)
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