I've had this happen a few times now. So I know I wasn't seeing things.
I had 7 shards of a single type of jewel. Level 1.
When I merged them it showed -4 and the leftovers disappeared.
They did NOT return with a refresh.

When next I merge jewels I'll make sure any spares are installed to avoid this newest "theft by code" scheme.

Yes, I am posting a billing support ticket as well.

Gorgon/various Arrows and Throwers