My thought on reconciling the kind of contradictory use of them as both pieces of the Silver Crystal and as prisons for the Seven Great Youma is as such: Serenity's Miracle (her "wish" as it came to be understood, causing everyone to be reincarnated) caused the Silver Crystal to be shattered into the seven gems we all know and love/loathe- but the Seven Youma didn't exist prior to that time. No, what happened is that a chunk of Silver Crystal came into conflict with something else in some person or other that corrupted it into the gems as we know them. Whether it was a current host or a previous one is largely inconsequential, save for one- Urawa Ryo ("Ryou", to distinguish from Sanada Ryo). Now why is he an exception? Because he has the potential to be a Trooper, but that's not important right now. The point of all of this is, something once broken can never truly be whole again, and this means two different things for the two different above-stated entities. For Arago, it means that he will never have his full form and power back, because the armors weren't just made from them, they've had a thousand years to develop on their own and we all know the old legend about objects gaining sentience at a certain age, and as for the Silver Crystal, it can never be Queen Serenity again. It can become someone/thing like her (NQS), but even as powerful as she is, she lacks the completeness, the unity, with the Crystal, because she isn't QS or PS, she's Usagi. A chunk of it that was broken off and had millennia and a whole human lifetime to shape into something of her own.