They stay there until you retrieve them, and then they go to your regular inventory. Any new mats go to your regular inventory.
Just some friendly advice, if you have not done so yet, roll 2 or 3 mule Alts and max out there Bag Spaces (both character and horse) to store all your crafting materials. Even more Alts if you have more than 200 of each material.
But can you retrieve them in small parts after it lapses or it takes them all out ?