Had an interesting interaction that my group could find no answer on during our Saturday game. The Crown of Thanlos agenda allows you to re-roll ANY dice, and any ship that does not produce a hit with its re-roll is destroyed. Now, if you're using this card to re-roll dice with a ship that throws more than one combat die (it was a flagship, in this situation), and your re-roll result gives you one hit and one miss, does the ship get destroyed? It did produce a result that was not a hit, but it also provided a result that was a hit.

All you need to be able to do is generate one hit with the reroll with that ship. In your example since you rerolled 2 dice which yielded at least 1 hit you are ok. If both dice missed then you would destroy your ship.