The blacksmith does not enchant anything. The enchanter does. He is found in the area west of Lovis's tower. When you bring new recipes to him they're removed from your inventory and saved to the enchantment list. Same goes for the tree. If your worried you could just save, sell the recipes, then check the tree to see if their still there.
You also don't need to save all the creature parts. Sell the weaker ones. Like if one pair of arms gives a 60% HP increase and another gives 70%, you should sell the 60% one.
