We have no clue. It's likely that they're stuck into the soulgems until used, but after that... we're not sure if the soul is destroyed by enchanting or recharging, or if it's returned to Atherius/Oblivion and the energy used in enchanting/recharging is actually the result of the soul peircing whatever seperates Mundus from Atherius/Oblivion.
Well we have some clues.
Umbra is still sentient within the weapon, but may be a special case on account of it is a chunk of Daedra. The Azura's Star quest in Skyrim implies that souls are still aware within their soulgems as well. I take these two points to mean that the dude you put in a black soul gem and enchanted a sword with is now your sword.
But enchantments fade and return sometimes, it seems. Just look at Volendrung.