Let me make it clear so there is no misunderstanding

If you refine with vanila item (with no properties) with item with extra properies (echant, protect, skin, timed, etc) the result item will always have the extra properties carried over no matter what is your inventory order

but if you have two items with extra properties you want to refine, you need to be careful with your item order in your inventory

For example

1. inventory a with enchant 100 with skin animal and inventory b with no extra properties
the result will be refined item with enchant 100 with skin animal

2. inventory a with enchant 100 with skin animal and inventory b with enchant 50
the result will be a refined item with 50 enchant with skin animal

3. inventory a with enchant 100 with skin animal and 100 protection and inventory b with enchant 50 with skin flower and 5 protection
the result will be a refined item with 50 enchant with skin flower and 5 protection

So the inventory b will always override the a inventory item if has extra properties as inventory a, if b dont have extra properties then a will keep theirs, thats why we recommend to only refine with vanilla item with no extra properties

Thank you