Congrats on the unique sale! Sounds like the buyer loves your product and has, essentially, invested in a relationship with you.
I would do as you suggest and make a listing for this year's stone addition. You can re-list it yearly. Charge as you do for your other items -- materials, labor, profit, etc. If you haven't sent the necklace/stone yet, I would enclose with it a small birthday card (or at least a note) with a business card and invitation to visit your shop next year to add to her necklace. If there are any special instructions around the stone addition to add (how to ship, etc), include them there and save a copy for both of your reference. That way, the burden to return lies on her and you don't have to keep track of this customer in a year.
Another option is to do like flower companies and other subscription services do and have the buyer purchase a few years' worth at a time. Then, the burden lies on you to remember to send the item for the next few years.
Personally, I would sell for the "now" (as Casi suggested) and encourage the customer to return, with a complete explanation of how things would proceed.
