When a stone disappears if is not a good match for you at the time, it's job in your life is finished, or it didn't like you to begin with (perhaps you misused/abused it). It will be found if and when it is right for you again. This is within the belief that stones and crystals have a spirit.
It isn't stolen, it is probably somewhere in your home. You may never find it or you may constantly find it and lose it again. I would say that whatever "intense spells" you did were not beneficial and such endeavors should be halted.
Spirits do not "steal" things. The most that they do is influence and trick our minds into overlooking the object or absent mindedly relocating it. How many times have you lost your keys, remote, cell phone, etc? No one ran off with it, it was merely mindlessly moved by you or slipped/fell while you were oblivious to it. And when you look for it, you overlook it 5-10 times. Spirits can at times utilize this flaw in our perception for their own entertainment or to relay a message. It's the same method we use when working the major misnomer, "invisibility" spells.