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I'm not sure about the Reliquary part of what your asking, but you'll find the answer to that in Guide to Pathfinder Society Open Play rulebook on page 19.
For ease of play in Pathfinder Society, a masterwork item can always be upgraded to a +1 item without paying for the masterwork cost again. Instead, you pay the difference between the cost of the +1 item and that of the masterwork item. This rule also applies to upgrading from a +1 item to a +2 item and so on—you never have to repay the original cost or sell your current item for half to upgrade to the next step. Note that this only applies to items of the same kind— you can’t, for example, turn your masterwork rapier into a +1 greatsword. A mundane item can not be upgraded to masterwork, nor can nonmagical aspects of equipment be upgraded (such as the strength rating on a composite bow).
It's always a good idea to have a copy of that document about as it contains the answers to a lot of questions. Hope that helps.

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I already have the Masterwork Great axe for 320gp. Do I sell it for 160gp and then purchase it for 2250 or can the 320 go against the upgrade and I can purchase it for 1930 gp?
Making a weapon a reliquary seems to be part of the enchanting process, which means you're in luck, just add the 250g on top of the enchantment. So if you already have the masterwork great axe then you'll only have to pay 2250.
Just remember when purchasing +1 equipment you need to factor in the cost of the masterwork item.
So a +1 great axe is 2320g (2000 for the +1, 320 for the masterwork great axe) and your +1 reliquary great axe actually costs 2570g
Also since this isn't a +1 weapon anymore you need to have enough fame(13) to make the purchase