AKA: Have I done something stupid?
I managed to hookup with a great PUG that ran all the SoS flagging quests which got me the 3 Dragonshard Essences. I then picked up my 3rd gem from the orchard. I thought I'd turn them all in to flag for the quest while I had them in my backpack, and then run the raid next time there was a LFM (not a guild member). What I didn't realise is Thear opened the portal for the quest then and there.
Have I just blown my gems?