This question has been bugging me for awhile. In MK:D Onaga supposedly kills Quan Chi and takes the amulet. However, Shujinko, Nightwolf, and Onaga's MK:A bios prove that Shujinko defeated Onaga at the end of MK:D, and there is no mention of it at all that I remember in MK:A. Shujinko's bio says that when Onaga is defeated, his body is reverted to Reptile. Onaga's MK:A bio also states that he still possessed the amulet when he was defeated. This means that Reptile has possession of the amulet at Deception's end. So, here are some possibilities as to the amulet's location:

1) After defeating Onaga, Shujinko discovers the amulet on Reptile's body. Now, either he would keep it for himself (unlikely) or give it to someone for safekeeping. One possibility is Fujin, as he is currently Earthrealm's protector god, and had guarded the amulet before. Another may be Kitana or Sindel, who (according to Shujinko's MK:A bio) became his allies. There is also the possibility that he returned it to Raiden. This is unlikely though as I get the impression from his MK:D ending that Raiden would have killed Shujinko on sight, and sadly he is still alive in MK:A. Also, I do not know if Raiden would have allied with Shinnok had he been in possession of the amulet, although he could use it as leverage in their agreement.

2) From Havik's MK:D ending I assume that he was present during the battle, and witnessed Onaga's defeat. Unfortunately his plan to steal the Dragon King's heart was in vain as he turned back into Reptile. It's possible however that he could have taken the amulet. I don't think Havik would have used it though, as he doesn't seem to be power hungry and tends to manipulate others towards his own ends. Because of this I think he may have given it to Kabal or Darrius.

3) Reptile regains consciousness and finds the amulet. I would assume that he would return to Shao Kahn's service after he finds out the emperor has returned. Since Shao Kahn is allied with Shinnok and the others, this would explain why Reptile is trying to close the portal in Daegon's base in MK:A. In this case Reptile would probably give the amulet to Kahn. Now the problem with this theory is that I find it unlikely that Kahn would ally with Quan Chi and Shinnok if he had the amulet in his possession.

4) Quan Chi takes the amulet back from whoever has it. However, he appears to be serving Shinnok in MK:A, something that wouldn't likely happen if Quan Chi had the amulet. It's possible that Quan Chi was killed by Raiden and Shinnok agreed to restore his life in exchange for retrieving the amulet. In any case, the amulet returns to Shinnok.

5) Bypass the middle man - Shinnok retrieves the amulet himself. I don't know how he would be able to escape the Netherrealm. Maybe he gets one his henchmen to do it - which would bring us back to #4.

It makes the most sense to me for either Fujin or Shinnok to have it, but still I have no proof. Any thoughts?