This has happened twice in the same game now. I'm not sure but I think the last time it happened was after fighting some fampyrs, so maybe the whole incessant weapon switching during charm has something to do with it.

Something similar happened to me. I gave Eder the Arms Bearer talent, and he was walking with a sword and shield in his third slot. Then suddenly I noticed that the shield (one of the bounty reward unique wall shields) had vanished. Really annoying, especially since it was a unique item.