I don't believe that the vials will dissapear if there are in a chest, however one of the vials is in the possession of some ancient zombies and not in a chest. If you haven't fought them for we can return to the Halls of Stone and try that out. The item from the vials though it's not much of a reason to restart the game but if like to find everything you might consider restarting but give a last search to the Halls of Stone before you do that.
And welcome to the boards. 
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"When I am working on a problem I never think about beauty. I only think about how to solve the problem. But when I have finished, if the solution is not beautiful, I know it is wrong."
Buckminster Fuller |