» Mon Jun 11, 2012 12:19 pm
This is a known bug. If you take everything from the container at once (the R key on the PC) the soul is preserved, but if you take items individually and you do not have a matching item (gem size, soul size, and price) in your inventory already, the soul is lost.
The way I deal with it is to have a container dedicated to just soul gems and always only use the Take all command when taking my soul gem out. I also save the game before doing the transfer, just in case.