Every time I adjust the appearance or color of any item I make sure to unequip it and reequip it. This doesn't just happen with armor, it happens with skill points increases from other items also.
I think it's because the way the Amia crafting system works, it destroys the item you are actually wearing (ever notice that dialog that you have lost X, or if you have the item quick slotted the slot empties?). Then when you finish crafting it doesn't reapply the benefits.
It's not too hard though to make the last action of crafting unequiping then reequiping the item.

It probably should be noted in the crafting dialog though.