Promise necklace **SPOILERS**

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-You're meshuga!
-I am not your sugar.
The Party

My own interpretation is that the whole movie is all a simulation. As in: EVERYTHING from the opening credits. They were abducted at an earlier point and had had a number of other simulations previously. There are a bunch of other threads that explain the total simulation idea.
If you agree with this then she never really threw the necklace. There was no necklace then and there wasn't later. It's all a big simulation and basically only the people are real and everything else is simulated in order to study the emotional reactions of humans. That's why he saw the necklace in his hand at that particularly emotional moment.
Makes sense?

I remember watching through that part thinking that I never actually saw her toss the necklace. If she did I must have missed it, but I assumed she just faked the throw and kept the necklace because she still had feelings for him

That necklace was a big clue that she wasn't real. She was probably a recreation to give him desire to free her and himself, finding the blend of human will and alien tech the aliens are seeking.