Weakened too much from his battle with the Warrior of Light? There isn't a super good reason, but we know Ascians are able to teleport in/out of that part of the Flagship so it isn't some kind of Allagan anti-teleport manuever. Why did Ascian prime disappear/teleport away only to return and split? There doesn't seem to be a good reason-- maybe Hydaelyn forces their hand somehow (they curse Hydaelyn before teleporting away, but that could mean almost anything given context)
It looks like there's some sort of charge-up time for them to flee to the Aetherial Rift, as Igeyorhm has enough time to publicly announce her intent to do so before we chuck the super rare and valuable white auracite at her.
(Also why is Nidhogg's left eye out of aether after that?? I guess the years of being used to channel the Azure Dragoon's power or something? The battle with Nidhogg/Azys Lla barrier I guess too, but man it seems a little ridiculous the Eye is stated to be so powerful but then is so quickly spent. It makes the Ascians/Allagans seem way stronger than dragons which isn't something I really got before as it took them teaming up to subdue Meracydia)
Thordan's bemoaning our use of "mortal contrivances" while simultaneously then yelling at Lahabrea for underestimating mortals bothers me as well but w/e w/e I'm off track
tl;dr: There's no good reason Lahabrea didn't flee. The best you could argue is that he didn't have enough stamina/power/Ascian juice left to do so, but Igeyorhm was about to do flee sooooooo yeah