Indeed. The VIth is now virtually extinct officially, given Regula's death, and the Gration is permenantly immobilized due to Ysayle's final sacrifice freezing the engines dead. So the Empire would have to divert a lot of resources to recover the ship and it's contingent of troops, which given their civil war and how Zenos has now seized control, they're simply not going to bother with it.

So the troops there are forever marooned, becoming yet another Imperial remnant force in Eorzea like the other Castri.