In patch 4.50 we learned from Emmanellain that Artoirel was with the Ishgardian army at Ghimlyt:

From 'The Face of War':
EMMANELLAIN
[Forename]! I thought you would be with the others defending the border at Ala Mhigo. I intended to volunteer my services, but alas, my dear brother was a few steps faster. With him gone, it falls to me to keep watch over House Fortemps.

HONOROIT
Worry not about Lord Emmanellain. He appeared devastated at the news that he could not venture to Ala Mhigo, that much is true. But deep down, I believe he is quite relieved that he can stay here at the manor.
Lining up with this, Artoirel is absent from his usual location outside Fortemps Manor.

Side note here: is "manor" the correct term for the hall at Camp Dragonhead (where these two characters have been located since 3.5), or did the scriptwriter here think they are still at Fortemps Manor in the city?



Patch 4.56 'A Requiem For Heroes' seems to introduce a time anomaly:
EDMONT
Speaking of fighting, you may be surprised to hear that the war's effects can already be felt even here in Ishgard. In anticipation of a need for reinforcements, Artoirel will soon be departing for the front lines with a contingent of our finest knights.


I'm guessing that the stories for 4.50 and 4.56 were originally drafted as a single sequence, but at some point they were split apart (creating an in-story time gap that wasn't originally intended to be there) and Emmanellain's dialogue change ended up on the wrong side of the split.



Less glaring, but something else that may have been caused by dividing the original script - when we first wake up in Ishgard, one of our dialogue choices is to specifically ask if Alisaie is okay. This makes sense if it followed soon after her being 'taken' in the scene after the Ghimlyt Dark dungeon, but seemed quite a strange option when it's been some time since that happened.