The enchantment formula are suppose to disappear. You'll have access to them once you get the enchant function working, and those formula will remain available for other enchanters later in the game. Actually, once you take over the battle tower (at a character level in the high teens or early twenties) you'll be able to use the machine there directly, without talking to the enchanter.
Are you sure you have equipment with enchantment slots, rather than charm slots? If there are any with enchantment slots, the equipment should be at the top of the Disenchantment list, with the proportion of filled and total enchantment slots shown to the right (it would be 0/1 or 1/1 for anything you've bought or found when you first reach the enchanter, and presumably not 0/1 or enchanting should work). Equipment with filled enchantment slots are shown in white text, while equipment with all empty enchantment slots or no enchantment slots are shown in light grey. Equipment without enchantment slots have nothing to the right of the name.
If you've disenchanted something, it should show up with a 0/1 in the Enchantment list, and you should be able to see the available enchantments, even if you don't have the ingredients.
