My end battle with the boss froze right at the end, she was defeatedm her goons were at 14 and 40 respectively, I attacked and the window froze. I tried to refresh and it just booted me from the battle, seemingly with no rewards.

That unfortunately is how it's coded to work. Once the event is no longer in existence, the zone becomes inaccessible and thus if you are in a battle, you can no longer access the zone. However, if you are still on the page in battle, you can continue. But if you leave (or an error/freezing causes you to leave), it will be unable to let you back in and will then close out your battle.

I will see what I can do to improve it and will try to get it implemented as soon as I can.