Is there a way to tell which Stone of Barenziah is found where?
Solution 1:
Without access to console/mods you are on your own to recheck all locations,note that there are few issues and in some cases they can be helpful.
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Periodically, some stones apparently respawn at their initial place, such as the one in Jarl Elisif the Fair's quarters(PS3/Xbox).
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In Calixto's House of Curiosities, it may be possible to obtain a stone at Calixto's museum on one of the shelves if every other location has been exhausted without obtaining all twenty-four(Xbox).
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There is a delay between when you click on the stone and when the stone is added to your inventory. If you click on a stone multiple times before it actually picks up, you will receive one stone but the quest will count it as two or more. This can be used to complete the quest faster as it does not affect the ability to move forward.
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If the Stone of Barenziah in Reeking Cave cannot be found beside the dead mage after applying Patch 1.4, a glitch will need to be utilized to reaccess the Thalmor Embassy and pick it up from its original location. This bug has been found in all versions of the game, and videos to resolve the situation are available on YouTube.
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For some reason, the gem may not appear on the counter where it supposed to sit in Fellglow Keep.
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The stone in Wuunferth the unliving's quarters may not be there after the quest Blood on the Ice. as of now, there is no known fix to this.
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For gems found inside dungeons where you might be fighting NPCs - they can be knocked off their table, shelf, pedestal or whatever by spells, arrows, bodies running into them, walking over them etc. and sometimes fall into inaccessible locations like a deep furrow in the ground or underneath furniture. In such a case, you may need to return to the area after a few in-game days and hope that the item locations are reset back to where they were at initially.
If somehow you are able to use mods these should do what you need,though I can't guarantee how they react when you've already found most of the stones... be careful with saved games.
https://www.nexusmods.com/skyrim/mods/9385
https://www.nexusmods.com/skyrim/mods/13274