Wait, this is better in the use proc

code/game/objects/items/stacks/stack.dm

@@ -225,8 +225,6 @@
 		if(O)
 			O.setDir(usr.dir)
 		use(R.req_amount * multiplier)
-		for(var/i in custom_materials)
-			custom_materials[i] = amount * mats_per_stack
 	
 		if(R.applies_mats && custom_materials && custom_materials.len)
 			var/list/used_materials = list()
@@ -317,6 +315,8 @@
 	amount -= used
 	if(check)
 		zero_amount()
+	for(var/i in custom_materials)
+		custom_materials[i] = amount * mats_per_stack
 	update_icon()
 	update_weight()
 	return TRUE