When I was swapping loadouts using the armory, some of my gems got downgraded.
Steps to recreate:
-Had loaded in armory: Helm with Flawless Royal diamond, Chest with 3x Flawless Royal topaz, legs with 2x open socket.
-Had equipped: Helm with Flawless Royal diamond, Chest with 3x Flawless Royal topaz, legs with 2x flawless royal topaz (only difference)
-Loaded the armory loadout
What happened: It unsocketed my pants, but gave me back 2 royal topazes (non-flawless, the stage before) instead of flawless royal topaz, effectively destroying 2/3 of my gems I had invested.
What was expected: It give me back 2 flawless royal topazes, the gems that were in the armor it unsocketed.
Other thoughts: I am not sure if this is specific to topazes, or this particular stage of this particular gem upgrades; I do not have the resources to exhaustively check every type of gem for this.