Shadow of the Vaal bugged, can't progress

During the killing of the act2 end boss the game crashed, so I reconnected and rejoined the party and killed the boss.

But this has completely bugged the shit out of the shadow of the vaal quest. Since I placed the apex in the altar I don't have it in my inventory, but the game won't recognise my boss kill as being legit.

So now I'm stuck in act 2 with no hope of progressing since nothing I can do will produce a new apex or permit my entry into Sarn.