I had a few of these in my inventory before I started the "No One Escapes Cidhna Mine" quest. When I got all my stuff back near the end of it I didn't have the gems (since they are considered stolen and confiscated). Now my question is, does this in any way affect the thieves guild mission for collecting 24 of them.

Nevermind, just found out that you get them back in your inventory as soon as the fighting starts. If an admin will please delete this.