Latias is a roaming legendary, which means she goes around the region and ends up in random places. I'd recommend going between two routes constantly, with a Repel up and your main Pokémon as level 40, so then the only Pokémon you'll encounter is Latias. When you encounter Latias after a while of running between routes, you should know that she will only stay there for one turn before running away again. I'd recommend getting a Pokémon with Mean Look to stop her from escaping, and then you can start using False Swipe to lower her health.
If you can't find a Pokémon with Mean Look, or if you're just too lazy like me, you can just throw your Masterball at Latias if you haven't already used it on something else.
Hope I helped!