At the end of the adventures it says:
In either event, make the changes listed below, then the Heroes may purchase any Advancements they wish at Port Nyanzaru.
I take this to mean that the Marketplace also comes after the decks are changed, so I put the new cards in and reshuffle before drawing the market treasures.
My question on this is whether you would ignore any Fortunes drawn and keep drawing until you reveal 4 Items, or just reveal 4 Treasure cards regardless of type. After my first adventure I drew 4 Fortunes, so there was nothing to buy at the market.