It's probably something as minor as a few dialogue changes. Same as 1.0 legacy WoL dialogue and those who started at 2.0?

From the screenshot preview it looks like Alisaie is making her way into the MSQ and since she and Alphinaud had some stuff go on in Final Coil, I assume there will be some minor dialogue to reflect it.

Same as the minor "we are fellow azure dragoon" type dialogue if you did DRG 50 when Estinien came back during that patch.