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Filled soul gems when placed into a container, such as a bedside table for example, can lose their souls if you take them back out of the container, and put them back into your inventory. This can usually only happen if you have empty soul gems of the same size, and value in your possession already. This is possibly because filled gems can get mixed back in with your empty ones due to some sort of bug. This can usually occur with Common, Lesser and Petty soul gems. This bug also happened a lot in Oblivion. It is recommended that you save your game before you move any filled and empty soul gems into your inventory from a container or likewise. Losing filled gems can be very annoying, so a possible work around for this is to use your follower to store the gems. For example, if you have a long list of full and empty soul gems in your inventory, and you want to stack the filled ones together without losing the souls; simply give them to your follower, and just take them back when needed. You hopefully shouldn't lose any of your souls this way.
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