Can the harmonic balance come loose?

I think you nailed it originally. I think it's the balancer, OR unfortunately, the crankshaft is broken in front of the first throw. It happens and it will keep running because the two pieces wedge together. Remove the balancer and you'll know for sure. I don't think it's the thrust bearing. No way would you be able to move the entire crank that easily with the engine still assembled. Either the balancer is broken, or the snout of the crank. Remove the balancer and you'll know.