That is ROUGH, I'm sorry.
I was reading about this bug online and you're definitely not alone in this. I'd suggest submitting a bug report to Larian. It's been bugged (pickpocketing, getting caught, gem disappearing) for several months. I don't know if they should have released Honour mode when the game is still so buggy.
Hopefully other folks can chime in if they've found a solution to this.
Edit: Would long resting help? Or did the shard drop on the floor somewhere?
