Similar Issue Report: After completing Zone 48 "Mesa Outpost", Zone 49 "Tree of Akhmora" was marked as Conquered
I completed Mesa Outpost, destroying all the cannons and killing all the warriors. The red bar reached correctly its maximum and the level gave me a "Success". However, after I returned to the Kromal world view, I discovered that Tree Of Akhmora was marked as "Conquered" instead.
Even after completing Mesa Outpost again, this level is still not marked as "Conquered".