item disappearing

When I allocated a passive to my amulet it disappeared

Can you be more specific? Are you saying the amulet itself is gone, the allocation mod on the amulet, the node on the passive tree? Things very, very rarely actually disappear, but they do tend to play hide and seek. Check every stash tab. You can do an "amulet" search to help highlight it. Also speak with Kirac. I think he still runs the official lost and found, but that's mostly from migration issues.

Even though this is posted in a PoE1 forum, it's probably a PoE2 issue due to how you enchant amulets there.

The crafting interface is opened by right-clicking a Distilled Emotion. If you don't remove the amulet after crafting, it stays in the crafting slot...so you have to right-click another Distilled Emotion to find it.