It's happened to me twice now on two different characters with different followers.

I'm travelling along with my companion wrecking whatever is in a dungeon....and then I turn to give her some loot and she's gone. Not dead. Gone. Poof. No corpse no nothing. I load up an autosave from the start of the dungeon where I KNOW she was with me. But she's STILL gone.

In Jordis' case I didn't notice till I got back to a town, but in Lydia's case she was litterally right behind me, shooting arrows at draugr one moment then the next she was just gone.

The first time this happened was with Jordis, during a civil war quest, the second time it happened to me was with Lydia in the Ansilvund Excavation. The only thing the two had in common that I can think of is that I'd buffed them with the courage spell around the same time it happened.

Other than that they had nothing in common, entirely different equipment and enchantment setups, Jordis was married my character Lydia wasn't, i wasn't even playing the same character with the two of them. My redguard was with Jordis and my imperial paladin traveled with Lydia..............The most distressing part is that loading an autosave from before the moment they vanished is NOT garunteed to fix it(usually doesn't actually). Autosave's have something weird going on at the moment where I've noticed some things seem to be persisting despite the load(changed equipment for example)

I loaded an autosave from before I opened a door into the deeper parts of the excavation site where lydia was still with me but when i loaded it she was still gone. The only way I've managed to get them to reappear is to load older saves from before wherever I started from.

I'm not sure what's causing the glitch but I'm guessing it has something to do with the courage spell. It's the only common thread I can think of and I played for awhile with Jordis before I started using the courage spell on her and it was soon after I started giving her the buff she vanished and my archer able to go an entire quest line with no problems with her follower(She doesn't use any buff spells for them).