With my first Earth-Encrusted Gem I bought “Cobalt Educator’s Knowledge” from Osidion, with my second I bought the black Court Patron’s Elegance.
Two days later, with my third Earth-Encrusted Gem I went back to Osidion. The Court Patron’s Elegance set was no longer available on the vendor, but the Cobalt Educator’s Knowledge was. I bought it, forgetting that I already had the set. This purchase incurred NO refund timer for the Earth-Encrusted Gem, and now I have an unusable “Cobalt Educator’s Knowledge” in my bags…
tl;dr Osidion does not always properly hide owned sets. It’s possible I bought it the first time on a different character? Either way, this means that it’s possible for Earth-Encrusted Gems to be entirely lost… Which is what happened to me.