I had an Amulet of Talos disappear when I had to give up my gear for the Cidhna Mine quest. When I got my gear back it was gone, but like 2 RL days later it was back in my personal inventory.

I also had something else disappear from my inventory (can't remember what it was now), but I chalked that up to accidentally selling it.

Dude! Totally happened to me as well, I thought I was going crazy and imagining it. I've had a few necklaces vanish completely, then reappear in my inventory. So I had to make another enchanted one, it was gone. Then poof, it's back. I suspected it was due to the Talos amulet being a quest item; the first time I equipped a talos amulet, my enchanted one disappeared.
I'm almost afraid to admit this because I might
really be crazy now, but I swear I've had a couple enchantments get switched around. One day I realized my gloves didn't have a lockpicking boost anymore; I knew it didn't make sense because I'd been opening difficult locks already for a long time... then suddenly bam, started breaking lockpicks, I was like okay what's going on here.
Had to make more enchanted gloves.