I got it right with mats being put in gear is not in any way refunded ever?
When you merge materials to gear or weapons, the sell price of the materials will be added to the gear or weapon. So when you sell stuff that contains materials, you'll get a higher price. You won't lose value when you craft.
So a new weapon with better base stats could be way worse than the ones you wear that has all slotted upgrades?
New weapons usually have a much higher upgrade potential. If you compare the last page in the item info, you'll see that the gear has more slots and more max slots which is very important.
However it's indeed possible that a new and better weapon in its basic form can have lower stats than you current gear, because no upgrades have been performed so far. But no worries, just buy the new gear, go to the blacksmith and merge your (in most cases better) materials into the empty slots and the new weapon will be better than your current one in no time.
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