Apparently there is a way to remove existing gems without destroying them.
Players can socket Onyx Annulet with Primordial Stones right after unlocking the item by bringing up its pop-up. The real challenge starts when it’s time to switch sockets. If you try to remove your initial sockets without progressing the quest line, you’ll have to break your existing sockets, essentially destroying them.
To remove sockets and keep them intact, fans must complete the Primordial Embellishment quest that will lead them to a Primordial Jeweler’s Kit. Upon finishing this quest, players can remove Gems without destroying them. Excess Primordial Stones can be exchanged for six Dormant Primordial Fragments that can be traded for new Stones from Researcher Imareth.