It is my understanding (according to this: http://elderscrolls.wikia.com/wiki/Soul_Cairn_(Dawnguard)) that the Soul Cairn only takes the souls of a used soul (meaning: soul used for enchanting a weapon or armor). The souls that are not yet used, remain in the soul gem, until it is broken (the soul is then free) or is used for enchanting (the remains of the soul go to the Soul Cairn for an eternity).

Thoughts on this?